BAli-Phy on XSEDE 3.2 BAli-Phy estimates multiple sequence alignments and evolutionary trees. Ben Redelings Redelings, B. (2014) Erasing Errors due to Alignment Ambiguity When Estimating Positive Selection. Molecular Biology and Evolution 31, 1979-1993 Suchard, M.A. and Redelings, B.D. BAli-Phy: Simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics, 22:2047-2048, 2006. Phylogeny / Alignment bali_phy3_xsede baliphy_comet perl "" 0 number_nodes 2 scheduler.conf perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" input_file Input File infile perl "infile" baliphy_verboseflag perl "-V" 10 all_results * runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours) 0.5 The maximum hours to run must be less than 168 perl $runtime > 168.0 The maximum hours to run must be greater than 0.05 perl $runtime < 0.05 perl "runhours=$value\\n" Values in the config file will be overwritten by values configured in the interface perl defined $config_file The job will run on 1 processor as configured. If it runs for the entire configured time, it will consume 1 X $runtime cpu hours perl $which_beast < 3 && $codon_partitioning && $nu_partitions eq 1 && !$no_beagle && !$datatype Estimate the maximum time your job will need to run. We recommend testimg initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. inputfile2_command perl defined $input_file2 2 perl "infile2" inputfile3_command perl defined $input_file3 3 perl "infile3" inputfile4_command perl defined $input_file4 4 perl "infile4" inputfile5_command perl defined $input_file5 4 perl "infile5" inputfile6_command perl defined $input_file6 4 perl "infile6" input_file2 Specify a second input file infile2 input_file3 Specify a third input file infile3 perl defined $input_file2 input_file4 Specify a fourth input file infile4 perl defined $input_file3 input_file5 Specify a fifth input file infile5 perl defined $input_file4 input_file6 Specify a sixth input file infile6 perl defined $input_file5 config_file Specify a config file perl (defined $value)" ? "--config config.txt":"" 5 config.txt tree_file Specify a starting tree perl (defined $value)" ? "--tree tree.tre":"" 6 tree.tre test_only Analyze the initial values and exit perl ($value) ? "--test":"" 20 directory_name Name for the analysis directory to create perl (defined $value) ? "-n $value":"" 33 num_iterations Number of iterations to run (-i) perl ($value != $vdef) ? "-i $value":"" 200000 30 Configure_Gene1 Configure Gene 1 analysis datatype Choose the data type for Gene 1 (--alphabet) 40 DNA RNA Amino-Acids Codons Triplets DNA "--alphabet 1:DNA" RNA "--alphabet 1:RNA" Amino-Acids "--alphabet 1:Amino-Acids" Codons "--alphabet 1:Codons" Triplets "--alphabet 1:Triplets" substitution_model Choose the Substitution Model for Gene 1 (-S) perl "-S 1:$value$gammarates41$invariable1" 50 f81 hky85 tn93 gtr HKYx3 TNx3 GTRx3 jtt wag lg08 gy94 gtr_sym+gy94 Sorry, the GTR, HKY85, and TN93 models can only be used for DNA or RNA data perl ($substitution_model eq "gtr" || $substitution_model eq "hky85" || $substitution_model eq "tn93" ) && (defined $datatype && $datatype ne "RNA" && $datatype ne "DNA") Sorry, the LG, JTT, and WAG models can only be used for Amino Acid data perl ($substitution_model eq "lg08" || $substitution_model eq "jtt" || $substitution_model eq "wag") && (defined $datatype && $datatype ne "Amino-Acids") Sorry, the HKYx3, TNx3, and GTRx3 models can only be used for Triplet data perl ($substitution_model eq "HKYx3" || $substitution_model eq " TNx3" || $substitution_model eq "GTRx3") && (defined $datatype && $datatype ne "Triplets") Sorry, the GY94 and GY94[GTR] models can only be used for Codon data perl ($substitution_model eq "gy94" || $substitution_model eq "gtr_sym+gy94") && (defined $datatype && $datatype ne "Codons") custom_model Enter a custom substitution model for Gene 1 perl "-S 1:$value" Sorry, you cant specify both a substitution model and a custom model perl defined $custom_model && $substitution_model 50 gammarates41 perl defined $substitution_model Use Gamma[4] for Gene 1 +Rates.gamma[4] invariable1 Allow invariant sites for Gene 1 perl defined $substitution_model +inv model_type_1 Estimate the insertion-deletion model for Gene 1 (-I) rs07 none rs07 "-I 1:rs07" none "-I 1:none" 60 Configure_Gene2 Configure Gene 2 analysis datatype_2 Choose the data type for Gene 2 (--alphabet) 41 perl defined $input_file2 DNA RNA Amino-Acids Codons Triplets DNA "--alphabet 2:DNA" RNA "--alphabet 2:RNA" Amino-Acids "--alphabet 2:Amino-Acids" Codons "--alphabet 2:Codons" Triplets "--alphabet 2:Triplets" substitution_model2 Choose the Substitution Model for Gene 2 (-S) perl defined $input_file2 perl "-S 2:$value$gammarates42$invariable2" 51 f81 hky85 tn93 gtr HKYx3 TNx3 GTRx3 jtt wag lg08 gy94 gtr_sym+gy94 Sorry, the GTR, HKY85, and TN93 models can only be used for DNA or RNA data perl ($substitution_model2 eq "gtr" || $substitution_model2 eq "hky85" || $substitution_model2 eq "tn93" ) && ($datatype_2 ne "RNA" && $datatype_2 ne "DNA") Sorry, the LG, JTT, and WAG models can only be used for Amino Acid data perl ($substitution_model2 eq "lg08" || $substitution_model2 eq "jtt" || $substitution_model2 eq "wag") && (defined $datatype_2 && $datatype_2 ne "Amino-Acids") Sorry, the HKYx3, TNx3, and GTRx3 models can only be used for Triplet data perl ($substitution_model2 eq "HKYx3" || $substitution_model2 eq " TNx3" || $substitution_model2 eq "GTRx3") && (defined $datatype_2 && $datatype_2 ne "Triplets") Sorry, the GY94 and GY94[GTR] models can only be used for Codon data perl ($substitution_model2 eq "gy94" || $substitution_model2 eq "gtr_sym+gy94") && (defined $datatype_2 && $datatype_2 ne "Codons") custom_model2 Enter a custom substitution model for Gene 2 perl defined $input_file2 perl "-S 2:$value" Sorry, you cant specify both a substitution model and a custom model perl defined $custom_model2 && $substitution_model2 51 gammarates42 Use Gamma[4] for Gene 2 perl defined $substitution_model2 +Rates.gamma[4] Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && ((defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && ((defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && ((defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && ((defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 6 && ((defined $invariable1 && !defined $invariable6) || (defined $invariable5 && !defined $invariable6)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && ((defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && ((defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && ((defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 6 && ((defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && ((defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && ((defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 6 && ((defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && ((defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 6 && ((defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && ((defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $gammarates42) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile23 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && ((defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && ((defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && ((defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && ((defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && ((defined $gammarates41 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates46)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && ((defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && ((defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && ((defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && ((defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && ((defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && ((defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && ((defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && ((defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && ((defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && ((defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && ((defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && ((defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && ((defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && ((defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && ((defined $invariable1 && !defined $invariable6) || (defined $invariable5 && !defined $invariable6)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && ((defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && ((defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && ((defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && ((defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && ((defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && ((defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && ((defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && ((defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && ((defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && ((defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) invariable2 Allow invariant sites for Gene 2 perl defined $substitution_model2 +inv model_type_2 Estimate the insertion-deletion model for Gene 2 (-I) perl defined $input_file2 rs07 none rs07 "-I 2:rs07" none "-I 2:none" 61 Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && defined $model_type_1 && defined $model_type_2 && ($model_type_1 ne $model_type_2) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && defined $model_type_1 && defined $model_type_3 && ($model_type_1 ne $model_type_3) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && defined $model_type_1 && defined $model_type_4 && ($model_type_1 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && defined $model_type_1 && defined $model_type_5 && ($model_type_1 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 6 && defined $model_type_1 && defined $model_type_6 && ($model_type_1 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && defined $model_type_2 && defined $model_type_3 && ($model_type_2 ne $model_type_3) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && defined $model_type_2 && defined $model_type_4 && ($model_type_2 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && defined $model_type_2 && defined $model_type_5 && ($model_type_2 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 6 && defined $model_type_2 && defined $model_type_6 && ($model_type_2 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && defined $model_type_3 && defined $model_type_4 && ($model_type_3 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && defined $model_type_3 && defined $model_type_5 && ($model_type_3 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 6 && defined $model_type_3 && defined $model_type_6 && ($model_type_3 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && defined $model_type_4 && defined $model_type_5 && ($model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 6 && defined $model_type_4 && defined $model_type_6 && ($model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 5 && $linkfile2 == 6 && defined $model_type_5 && defined $model_type_6 && ($model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_3 || $model_type_2 != $model_type_3 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && defined $model_type_1 && defined $model_type_2 && defined $model_type_4 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_4 || $model_type_2 != $model_type_4 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_5 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_5 || $model_type_2 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_6 || $model_type_2 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && defined $model_type_1 && defined $model_type_3 && defined $model_type_4 && ($model_type_1 != $model_type_3 || $model_type_1 != $model_type_4 || $model_type_3 != $model_type_4 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && defined $model_type_1 && defined $model_type_3 && defined $model_type_5 && ($model_type_1 != $model_type_3 || $model_type_1 != $model_type_5 || $model_type_3 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && defined $model_type_1 && defined $model_type_3 && defined $model_type_6 && ($model_type_1 != $model_type_3 || $model_type_1 != $model_type_6 || $model_type_3 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && defined $model_type_1 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 != $model_type_4 || $model_type_1 != $model_type_5 || $model_type_4 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && defined $model_type_1 && defined $model_type_4 && defined $model_type_6 && ($model_type_1 != $model_type_4 || $model_type_1 != $model_type_6 || $model_type_4 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && defined $model_type_1 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 != $model_type_5 || $model_type_1 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && ($model_type_2 != $model_type_3 || $model_type_2 != $model_type_4 || $model_type_3 != $model_type_4 ) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && defined $model_type_2 && defined $model_type_3 && defined $model_type_5 && ($model_type_2 != $model_type_3 || $model_type_2 != $model_type_5 || $model_type_3 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_6 && ($model_type_2 != $model_type_3 || $model_type_2 != $model_type_6 || $model_type_3 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && defined $model_type_2 && defined $model_type_4 && defined $model_type_5 && ($model_type_2 != $model_type_4 || $model_type_2 != $model_type_5 || $model_type_4 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && defined $model_type_2 && defined $model_type_4 && defined $model_type_6 && ($model_type_2 != $model_type_4 || $model_type_2 != $model_type_6 || $model_type_4 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && defined $model_type_2 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 != $model_type_5 || $model_type_2 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_3 != $model_type_4 || $model_type_3 != $model_type_5 || $model_type_4 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && defined $model_type_3 && defined $model_type_4 && defined $model_type_6 && ($model_type_3 != $model_type_4 || $model_type_3 != $model_type_6 || $model_type_4 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && defined $model_type_3 && defined $model_type_5 && defined $model_type_6 && ($model_type_3 != $model_type_5 || $model_type_3 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_4 != $model_type_5 || $model_type_4 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && ($model_type_1 ne $model_type_4 || $model_type_2 ne $model_type_4 || $model_type_3 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_2 ne $model_type_5 || $model_type_3 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_2 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_4 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $model_type_1 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_3 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $model_type_1 && defined $model_type_3 && defined $model_type_4 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $model_type_1 && defined $model_type_3 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $model_type_1 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_2 ne $model_type_5 || $model_type_3 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $model_type_2 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_2 ne $model_type_5 || $model_type_3 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && defined $model_type_1 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && defined $model_type_1 && defined $model_type_2 && ($model_type_1 ne $model_type_2) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && defined $model_type_1 && defined $model_type_3 && ($model_type_1 ne $model_type_3) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && defined $model_type_1 && defined $model_type_4 && ($model_type_1 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && defined $model_type_1 && defined $model_type_5 && ($model_type_1 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && defined $model_type_1 && defined $model_type_6 && ($model_type_1 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && defined $model_type_2 && defined $model_type_3 && ($model_type_2 ne $model_type_3) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && defined $model_type_2 && defined $model_type_4 && ($model_type_2 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && defined $model_type_2 && defined $model_type_5 && ($model_type_2 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && defined $model_type_2 && defined $model_type_6 && ($model_type_2 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && defined $model_type_3 && defined $model_type_4 && ($model_type_3 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && defined $model_type_3 && defined $model_type_5 && ($model_type_3 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && defined $model_type_3 && defined $model_type_6 && ($model_type_3 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && defined $model_type_4 && defined $model_type_5 && ($model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && defined $model_type_4 && defined $model_type_6 && ($model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 5 && $linkfile22 == 6 && defined $model_type_5 && defined $model_type_6 && ($model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_3 || $model_type_2 != $model_type_3 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && defined $model_type_1 && defined $model_type_2 && defined $model_type_4 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_4 || $model_type_2 != $model_type_4 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_5 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_5 || $model_type_2 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_6 || $model_type_2 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && defined $model_type_1 && defined $model_type_3 && defined $model_type_4 && ($model_type_1 != $model_type_3 || $model_type_1 != $model_type_4 || $model_type_3 != $model_type_4 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && defined $model_type_1 && defined $model_type_3 && defined $model_type_5 && ($model_type_1 != $model_type_3 || $model_type_1 != $model_type_5 || $model_type_3 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && defined $model_type_1 && defined $model_type_3 && defined $model_type_6 && ($model_type_1 != $model_type_3 || $model_type_1 != $model_type_6 || $model_type_3 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && defined $model_type_1 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 != $model_type_4 || $model_type_1 != $model_type_5 || $model_type_4 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && defined $model_type_1 && defined $model_type_4 && defined $model_type_6 && ($model_type_1 != $model_type_4 || $model_type_1 != $model_type_6 || $model_type_4 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && defined $model_type_1 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 != $model_type_5 || $model_type_1 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && ($model_type_2 != $model_type_3 || $model_type_2 != $model_type_4 || $model_type_3 != $model_type_4 ) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && defined $model_type_2 && defined $model_type_3 && defined $model_type_5 && ($model_type_2 != $model_type_3 || $model_type_2 != $model_type_5 || $model_type_3 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_6 && ($model_type_2 != $model_type_3 || $model_type_2 != $model_type_6 || $model_type_3 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && defined $model_type_2 && defined $model_type_4 && defined $model_type_5 && ($model_type_2 != $model_type_4 || $model_type_2 != $model_type_5 || $model_type_4 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && defined $model_type_2 && defined $model_type_4 && defined $model_type_6 && ($model_type_2 != $model_type_4 || $model_type_2 != $model_type_6 || $model_type_4 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && defined $model_type_2 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 != $model_type_5 || $model_type_2 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_3 != $model_type_4 || $model_type_3 != $model_type_5 || $model_type_4 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && defined $model_type_3 && defined $model_type_4 && defined $model_type_6 && ($model_type_3 != $model_type_4 || $model_type_3 != $model_type_6 || $model_type_4 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && defined $model_type_3 && defined $model_type_5 && defined $model_type_6 && ($model_type_3 != $model_type_5 || $model_type_3 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_4 != $model_type_5 || $model_type_4 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && ($model_type_1 ne $model_type_4 || $model_type_2 ne $model_type_4 || $model_type_3 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_2 ne $model_type_5 || $model_type_3 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_2 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_4 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $model_type_1 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_3 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $model_type_1 && defined $model_type_3 && defined $model_type_4 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $model_type_1 && defined $model_type_3 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $model_type_1 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_2 ne $model_type_5 || $model_type_3 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $model_type_2 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Configure_Gene3 Configure Gene 3 analysis datatype_3 Choose the data type for Gene 3 (--alphabet) 42 perl defined $input_file3 DNA RNA Amino-Acids Codons Triplets DNA "--alphabet 3:DNA" RNA "--alphabet 3:RNA" Amino-Acids "--alphabet 3:Amino-Acids" Codons "--alphabet 3:Codons" Triplets "--alphabet 3:Triplets" substitution_model3 Choose the Substitution Model for Gene 3 (-S) perl defined $input_file3 perl "-S 3:$value$gammarates43$invariable3" 52 f81 hky85 tn93 gtr HKYx3 TNx3 GTRx3 jtt wag lg08 gy94 gtr_sym+gy94 Sorry, the GTR, HKY85, and TN93 models can only be used for DNA or RNA data perl ($substitution_model3 eq "gtr" || $substitution_model3 eq "hky85" || $substitution_model3 eq "tn93" ) && (defined $datatype_3 && $datatype_3 ne "RNA" && $datatype_3 ne "DNA") Sorry, the LG, JTT, and WAG models can only be used for Amino Acid data perl ($substitution_model3 eq "lg08" || $substitution_model3 eq "jtt" || $substitution_model3 eq "wag") && (defined $datatype_3 && $datatype_3 ne "Amino-Acids") Sorry, the HKYx3, TNx3, and GTRx3 models can only be used for Triplet data perl ($substitution_model3 eq "HKYx3" || $substitution_model3 eq " TNx3" || $substitution_model3 eq "GTRx3") && (defined $datatype_3 && $datatype_3 ne "Triplets") Sorry, the GY94 and GY94[GTR] models can only be used for Codon data perl ($substitution_model3 eq "gy94" || $substitution_model3 eq "gtr_sym+gy94") && (defined $datatype_3 && $datatype_3 ne "Codons") custom_model3 Enter a custom substitution model for Gene 3 perl defined $input_file3 perl "-S 3:$value" Sorry, you cant specify both a substitution model and a custom model perl defined $custom_model3 && $substitution_model3 52 gammarates43 Use Gamma[4] for Gene 3 perl defined $substitution_model3 +Rates.gamma[4] invariable3 Allow invariant sites for Gene 3 perl defined $substitution_model3 +inv model_type_3 Estimate the insertion-deletion model for Gene 3 (-I) perl defined $input_file3 rs07 none rs07 "-I 3:rs07" none "-I 3:none" 62 Configure_Gene4 Configure Gene 4 analysis datatype_4 Choose the data type for Gene 4 (--alphabet) 43 perl defined $input_file4 DNA RNA Amino-Acids Codons Triplets DNA "--alphabet 4:DNA" RNA "--alphabet 4:RNA" Amino-Acids "--alphabet 4:Amino-Acids" Codons "--alphabet 4:Codons" Triplets "--alphabet 4:Triplets" substitution_model4 Choose the Substitution Model for Gene 4 (-S) perl defined $input_file4 perl "-S 4:$value$gammarates44$invariable4" 53 f81 hky85 tn93 gtr HKYx3 TNx3 GTRx3 jtt wag lg08 gy94 gtr_sym+gy94 Sorry, the GTR, HKY85, and TN93 models can only be used for DNA or RNA data perl ($substitution_model4 eq "gtr" || $substitution_model4 eq "hky85" || $substitution_model4 eq "tn93" ) && (defined $datatype_4 && $datatype_4 ne "RNA" && $datatype_4 ne "DNA") Sorry, the LG, JTT, and WAG models can only be used for Amino Acid data perl ($substitution_model4 eq "lg08" || $substitution_model4 eq "jtt" || $substitution_model4 eq "wag") && (defined $datatype_4 && $datatype_4 ne "Amino-Acids") Sorry, the HKYx3, TNx3, and GTRx3 models can only be used for Triplet data perl ($substitution_model4 eq "HKYx3" || $substitution_model4 eq " TNx3" || $substitution_model4 eq "GTRx3") && (defined $datatype_4 && $datatype_4 ne "Triplets") Sorry, the GY94 and GY94[GTR] models can only be used for Codon data perl ($substitution_model4 eq "gy94" || $substitution_model4 eq "gtr_sym+gy94") && (defined $datatype_4 && $datatype_4 ne "Codons") custom_model4 Enter a custom substitution model for Gene 4 perl defined $input_file4 perl "-S 4:$value" Sorry, you cant specify both a substitution model and a custom model perl defined $custom_model4 && $substitution_model4 53 gammarates44 Use Gamma[4] for Gene 4 perl defined $substitution_model4 +Rates.gamma[4] invariable4 Allow invariant sites for Gene 4 perl defined $substitution_model4 +inv model_type_4 Estimate the insertion-deletion model for Gene 4 (-I) perl defined $input_file4 rs07 none rs07 "-I 4:rs07" none "-I 4:none" 63 Configure_Gene5 Configure Gene 5 analysis datatype_5 Choose the data type for Gene 5 (--alphabet) 44 perl defined $input_file5 DNA RNA Amino-Acids Codons Triplets DNA "--alphabet 5:DNA" RNA "--alphabet 5:RNA" Amino-Acids "--alphabet 5:Amino-Acids" Codons "--alphabet 5:Codons" Triplets "--alphabet 5:Triplets" substitution_model5 Choose the Substitution Model for Gene 5 (-S) perl defined $input_file5 perl "-S 5:$value$gammarates45$invariable5" 54 f81 hky85 tn93 gtr HKYx3 TNx3 GTRx3 jtt wag lg08 gy94 gtr_sym+gy94 Sorry, the GTR, HKY85, and TN93 models can only be used for DNA or RNA data perl ($substitution_model5 eq "gtr" || $substitution_model5 eq "hky85" || $substitution_model5 eq "tn93" ) && (defined $datatype_5 && $datatype_5 ne "RNA" && $datatype_5 ne "DNA") Sorry, the LG, JTT, and WAG models can only be used for Amino Acid data perl ($substitution_model5 eq "lg08" || $substitution_model5 eq "jtt" || $substitution_model5 eq "wag") && (defined $datatype_5 && $datatype_5 ne "Amino-Acids") Sorry, the HKYx3, TNx3, and GTRx3 models can only be used for Triplet data perl ($substitution_model5 eq "HKYx3" || $substitution_model5 eq " TNx3" || $substitution_model5 eq "GTRx3") && (defined $datatype_5 && $datatype_5 ne "Triplets") Sorry, the GY94 and GY94[GTR] models can only be used for Codon data perl ($substitution_model5 eq "gy94" || $substitution_model5 eq "gtr_sym+gy94") && (defined $datatype_5 && $datatype_5 ne "Codons") custom_model5 Enter a custom substitution model for Gene 5 perl defined $input_file5 perl "-S 5:$value" Sorry, you cant specify both a substitution model and a custom model perl defined $custom_model5 && $substitution_model5 54 gammarates45 Use Gamma[4] for Gene 5 perl defined $substitution_model5 +Rates.gamma[4] invariable5 Allow invariant sites for Gene 5 perl defined $substitution_model5 +inv model_type_5 Estimate the insertion-deletion model for Gene 5 (-I) perl defined $input_file5 rs07 none rs07 "-I 5:rs07" none "-I 5:none" 64 Configure_Gene6 Configure Gene 6 analysis datatype_6 Choose the data type for Gene 6 (--alphabet) 45 perl defined $input_file6 DNA RNA Amino-Acids Codons Triplets DNA "--alphabet 6:DNA" RNA "--alphabet 6:RNA" Amino-Acids "--alphabet 6:Amino-Acids" Codons "--alphabet 6:Codons" Triplets "--alphabet 6:Triplets" substitution_model6 Choose the Substitution Model for Gene 6 (-S) perl defined $input_file6 perl "-S 6:$value$gammarates46$invariable6" 55 f81 hky85 tn93 gtr HKYx3 TNx3 GTRx3 jtt wag lg08 gy94 gtr_sym+gy94 Sorry, the GTR, HKY85, and TN93 models can only be used for DNA or RNA data perl ($substitution_model6 eq "gtr" || $substitution_model6 eq "hky85" || $substitution_model6 eq "tn93" ) && (defined $datatype_6 && $datatype_6 ne "RNA" && $datatype_6 ne "DNA") Sorry, the LG, JTT, and WAG models can only be used for Amino Acid data perl ($substitution_model6 eq "lg08" || $substitution_model6 eq "jtt" || $substitution_model6 eq "wag") && (defined $datatype_6 && $datatype_6 ne "Amino-Acids") Sorry, the HKYx3, TNx3, and GTRx3 models can only be used for Triplet data perl ($substitution_model6 eq "HKYx3" || $substitution_model6 eq " TNx3" || $substitution_model6 eq "GTRx3") && (defined $datatype_6 && $datatype_6 ne "Triplets") Sorry, the GY94 and GY94[GTR] models can only be used for Codon data perl ($substitution_model6 eq "gy94" || $substitution_model6 eq "gtr_sym+gy94") && (defined $datatype_6 && $datatype_6 ne "Codons") custom_model6 Enter a custom substitution model for Gene 6 perl defined $input_file6 perl "-S 6:$value" Sorry, you cant specify both a substitution model and a custom model perl defined $custom_model6 && $substitution_model6 55 gammarates46 Use Gamma[4] for Gene 6 perl defined $substitution_model6 +Rates.gamma[4] invariable6 Allow invariant sites for Gene 6 perl defined $substitution_model6 +inv model_type_6 Estimate the insertion-deletion model for Gene 6 (-I) perl defined $input_file6 rs07 none rs07 "-I 6:rs07" none "-I 6:none" 65 mcmc_options Model Options subsample_factor Factor by which to subsample (-x) perl ($value != $vdef) ? "-x $value":"" 1 31 The optimal value for subsample factor is one in most cases perl $subsample_factor != "1" The number supplied here determines how often to sample. For example -x 10 keep every 10th sample. 1 is the best value random_seed Random seed (-s) perl defined $value ? "-s $value":"" 32 Specify a seed to make individual runs identical link_specified_h perl defined $linkfile1 && defined $linkfile2 && !defined $linkfile3 perl "--link $linkfile1,$linkfile2:" 70 link_specified_h2 perl defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && !defined $linkfile4 perl "--link $linkfile1,$linkfile2,$linkfile3:" 70 link_specified_h3 perl defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && !defined $linkfile5 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4:" 70 link_specified_h4 perl defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && !defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,linkfile5:" 70 link_specified_h5 perl defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,$linkfile5,$linkfile6:" 70 link_specified_h21 perl defined $linkfile21 && defined $linkfile22 && !defined $linkfile23 perl "--link $linkfile21,$linkfile22:" 70 link_specified_h22 perl defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && !defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23:" 70 link_specified_h23 perl defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23,$linkfile24:" 70 link_models Linking model options Select a group of Genes to Link Select a group of Genes to Link linkfile1 Select the first gene to link (choose the lowest value first) 1 2 3 4 5 6 Please enter the lowest gene number first perl $linkfile1 > $linkfile2 Sorry, a given gene can only be linked once perl defined $linkfile1 && defined $linkfile2 && ($linkfile1 eq $linkfile21 || $linkfile1 eq $linkfile22 || $linkfile2 eq $linkfile21 || $linkfile2 eq $linkfile22 ) Sorry, a given gene can only be linked once perl defined $linkfile1 && defined $linkfile2 && ($linkfile1 eq $linkfile23 || $linkfile1 eq $linkfile24 || $linkfile2 eq $linkfile23 || $linkfile2 eq $linkfile24 ) Sorry, the same gene cannot be linked twice to the same group perl defined $linkfile1 && defined $linkfile2 && ($linkfile1 eq $linkfile2) Please select at least one more gene (up to six) to link perl defined $linkfile1 && !defined $linkfile2 Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && defined $datatype && defined $datatype_2 && ($datatype ne $datatype_2) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && defined $datatype && defined $datatype_3 && ($datatype ne $datatype_3) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && defined $datatype && defined $datatype_4 && ($datatype ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && defined $datatype && defined $datatype_5 && ($datatype ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 6 && defined $datatype && defined $datatype_6 && ($datatype ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && defined $datatype_2 && defined $datatype_3 && ($datatype_2 ne $datatype_3) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && defined $datatype_2 && defined $datatype_4 && ($datatype_2 ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && defined $datatype_2 && defined $datatype_5 && ($datatype_2 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 6 && defined $datatype_2 && defined $datatype_6 && ($datatype_2 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && defined $datatype_3 && defined $datatype_4 && ($datatype_3 ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && defined $datatype_3 && defined $datatype_5 && ($datatype_3 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 6 && defined $datatype_3 && defined $datatype_6 && ($datatype_3 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && defined $datatype_4 && defined $datatype_5 && ($datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 6 && defined $datatype_4 && defined $datatype_6 && ($datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 5 && $linkfile2 == 6 && defined $datatype_5 && defined $datatype_6 && ($datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && defined $datatype && defined $datatype_2 && defined $datatype_3 && ($datatype != $datatype_2 || $datatype != $datatype_3 || $datatype_2 != $datatype_3 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && defined $datatype && defined $datatype_2 && defined $datatype_4 && ($datatype != $datatype_2 || $datatype != $datatype_4 || $datatype_2 != $datatype_4 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_5 && ($datatype != $datatype_2 || $datatype != $datatype_5 || $datatype_2 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_3 && ($datatype != $datatype_2 || $datatype != $datatype_6 || $datatype_2 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && defined $datatype && defined $datatype_3 && defined $datatype_4 && ($datatype != $datatype_3 || $datatype != $datatype_4 || $datatype_3 != $datatype_4 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && defined $datatype && defined $datatype_3 && defined $datatype_5 && ($datatype != $datatype_3 || $datatype != $datatype_5 || $datatype_3 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && defined $datatype && defined $datatype_3 && defined $datatype_6 && ($datatype != $datatype_3 || $datatype != $datatype_6 || $datatype_3 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && defined $datatype && defined $datatype_4 && defined $datatype_5 && ($datatype != $datatype_4 || $datatype != $datatype_5 || $datatype_4 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && defined $datatype && defined $datatype_4 && defined $datatype_6 && ($datatype != $datatype_4 || $datatype != $datatype_6 || $datatype_4 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && defined $datatype && defined $datatype_5 && defined $datatype_6 && ($datatype != $datatype_5 || $datatype != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && ($datatype_2 != $datatype_3 || $datatype_2 != $datatype_4 || $datatype_3 != $datatype_4 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && ($datatype_2 != $datatype_3 || $datatype_2 != $datatype_5 || $datatype_3 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_6 && ($datatype_2 != $datatype_3 || $datatype_2 != $datatype_6 || $datatype_3 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && defined $datatype_2 && defined $datatype_4 && defined $datatype_5 && ($datatype_2 != $datatype_4 || $datatype_2 != $datatype_5 || $datatype_4 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && defined $datatype_2 && defined $datatype_4 && defined $datatype_6 && ($datatype_2 != $datatype_4 || $datatype_2 != $datatype_6 || $datatype_4 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && defined $datatype_2 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 != $datatype_5 || $datatype_2 != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype_3 != $datatype_4 || $datatype_3 != $datatype_5 || $datatype_4 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && defined $datatype_3 && defined $datatype_4 && defined $datatype_6 && ($datatype_3 != $datatype_4 || $datatype_3 != $datatype_6 || $datatype_4 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype_3 != $datatype_5 || $datatype_3 != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_4 != $datatype_5 || $datatype_4 != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && ($datatype ne $datatype_4 || $datatype_2 ne $datatype_4 || $datatype_3 ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_2 ne $datatype_5 || $datatype_3 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_4 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_2 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_4 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $datatype && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_3 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $datatype && defined $datatype_3 && defined $datatype_4 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $datatype && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $datatype && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype_2 ne $datatype_5 || $datatype_3 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $datatype_2 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_2 ne $datatype_5 || $datatype_3 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && defined $datatype && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && defined $substitution_model && defined $substitution_model2 && ($substitution_model ne $substitution_model2) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && defined $substitution_model && defined $substitution_model3 && ($substitution_model ne $substitution_model3) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && defined $substitution_model && defined $substitution_model4 && ($substitution_model ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && defined $substitution_model && defined $substitution_model5 && ($substitution_model ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 6 && defined $substitution_model && defined $substitution_model6 && ($substitution_model ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && defined $substitution_model2 && defined $substitution_model3 && ($substitution_model2 ne $substitution_model3) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && defined $substitution_model2 && defined $substitution_model4 && ($substitution_model2 ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && defined $substitution_model2 && defined $substitution_model5 && ($substitution_model2 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 6 && defined $substitution_model2 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model3 ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model3 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 6 && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model3 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 6 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 5 && $linkfile2 == 6 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model3 || $substitution_model2 != $substitution_model3 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model4 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model4 || $substitution_model2 != $substitution_model4 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model5 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model5 || $substitution_model2 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model6 || $substitution_model2 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model != $substitution_model3 || $substitution_model != $substitution_model4 || $substitution_model3 != $substitution_model4 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model != $substitution_model3 || $substitution_model != $substitution_model5 || $substitution_model3 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model != $substitution_model3 || $substitution_model != $substitution_model6 || $substitution_model3 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && defined $substitution_model && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model != $substitution_model4 || $substitution_model != $substitution_model5 || $substitution_model4 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && defined $substitution_model && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model != $substitution_model4 || $substitution_model != $substitution_model6 || $substitution_model4 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && defined $substitution_model && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model != $substitution_model5 || $substitution_model != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model2 != $substitution_model3 || $substitution_model2 != $substitution_model4 || $substitution_model3 != $substitution_model4 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model2 != $substitution_model3 || $substitution_model2 != $substitution_model5 || $substitution_model3 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model2 != $substitution_model3 || $substitution_model2 != $substitution_model6 || $substitution_model3 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model2 != $substitution_model4 || $substitution_model2 != $substitution_model5 || $substitution_model4 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model2 != $substitution_model4 || $substitution_model2 != $substitution_model6 || $substitution_model4 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && defined $substitution_model2 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 != $substitution_model5 || $substitution_model2 != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model3 != $substitution_model4 || $substitution_model3 != $substitution_model5 || $substitution_model4 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model3 != $substitution_model4 || $substitution_model3 != $substitution_model6 || $substitution_model4 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && defined $substitution_model3 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model3 != $substitution_model5 || $substitution_model3 != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model4 != $substitution_model5 || $substitution_model4 != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model ne $substitution_model4 || $substitution_model2 ne $substitution_model4 || $substitution_model3 ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model2 ne $substitution_model5 || $substitution_model3 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model2 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model3 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $substitution_model && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model2 ne $substitution_model5 || $substitution_model3 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model2 ne $substitution_model5 || $substitution_model3 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && defined $substitution_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) linkfile2 Select the second gene to link (--link) 1 2 3 4 5 6 Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && defined $custom_model && defined $custom_model2 && ($custom_model ne $custom_model2) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && defined $custom_model && defined $custom_model3 && ($custom_model ne $custom_model3) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && defined $custom_model && defined $custom_model4 && ($custom_model ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && defined $custom_model && defined $custom_model5 && ($custom_model ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 6 && defined $custom_model && defined $custom_model6 && ($custom_model ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && defined $custom_model2 && defined $custom_model3 && ($custom_model2 ne $custom_model3) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && defined $custom_model2 && defined $custom_model4 && ($custom_model2 ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && defined $custom_model2 && defined $custom_model5 && ($custom_model2 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 6 && defined $custom_model2 && defined $custom_model6 && ($custom_model2 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && defined $custom_model3 && defined $custom_model4 && ($custom_model3 ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && defined $custom_model3 && defined $custom_model5 && ($custom_model3 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 6 && defined $custom_model3 && defined $custom_model6 && ($custom_model3 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && defined $custom_model4 && defined $custom_model5 && ($custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 6 && defined $custom_model4 && defined $custom_model6 && ($custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 5 && $linkfile2 == 6 && defined $custom_model5 && defined $custom_model6 && ($custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && ($custom_model != $custom_model2 || $custom_model != $custom_model3 || $custom_model2 != $custom_model3 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && defined $custom_model && defined $custom_model2 && defined $custom_model4 && ($custom_model != $custom_model2 || $custom_model != $custom_model4 || $custom_model2 != $custom_model4 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model5 && ($custom_model != $custom_model2 || $custom_model != $custom_model5 || $custom_model2 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && ($custom_model != $custom_model2 || $custom_model != $custom_model6 || $custom_model2 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && defined $custom_model && defined $custom_model3 && defined $custom_model4 && ($custom_model != $custom_model3 || $custom_model != $custom_model4 || $custom_model3 != $custom_model4 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && defined $custom_model && defined $custom_model3 && defined $custom_model5 && ($custom_model != $custom_model3 || $custom_model != $custom_model5 || $custom_model3 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && defined $custom_model && defined $custom_model3 && defined $custom_model6 && ($custom_model != $custom_model3 || $custom_model != $custom_model6 || $custom_model3 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && defined $custom_model && defined $custom_model4 && defined $custom_model5 && ($custom_model != $custom_model4 || $custom_model != $custom_model5 || $custom_model4 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && defined $custom_model && defined $custom_model4 && defined $custom_model6 && ($custom_model != $custom_model4 || $custom_model != $custom_model6 || $custom_model4 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && defined $custom_model && defined $custom_model5 && defined $custom_model6 && ($custom_model != $custom_model5 || $custom_model != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && ($custom_model2 != $custom_model3 || $custom_model2 != $custom_model4 || $custom_model3 != $custom_model4 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && defined $custom_model2 && defined $custom_model3 && defined $custom_model5 && ($custom_model2 != $custom_model3 || $custom_model2 != $custom_model5 || $custom_model3 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model6 && ($custom_model2 != $custom_model3 || $custom_model2 != $custom_model6 || $custom_model3 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && defined $custom_model2 && defined $custom_model4 && defined $custom_model5 && ($custom_model2 != $custom_model4 || $custom_model2 != $custom_model5 || $custom_model4 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && defined $custom_model2 && defined $custom_model4 && defined $custom_model6 && ($custom_model2 != $custom_model4 || $custom_model2 != $custom_model6 || $custom_model4 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && defined $custom_model2 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 != $custom_model5 || $custom_model2 != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model3 != $custom_model4 || $custom_model3 != $custom_model5 || $custom_model4 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model3 != $custom_model4 || $custom_model3 != $custom_model6 || $custom_model4 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && defined $custom_model3 && defined $custom_model5 && defined $custom_model6 && ($custom_model3 != $custom_model5 || $custom_model3 != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model4 != $custom_model5 || $custom_model4 != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && ($custom_model ne $custom_model4 || $custom_model2 ne $custom_model4 || $custom_model3 ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model2 ne $custom_model5 || $custom_model3 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model4 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model2 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $custom_model && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model3 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $custom_model && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $custom_model && defined $custom_model3 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $custom_model && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model2 ne $custom_model5 || $custom_model3 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $custom_model2 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model2 ne $custom_model5 || $custom_model3 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && ((defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && ((defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && ((defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && ((defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 6 && ((defined $gammarates41 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates46)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && ((defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && ((defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && ((defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 6 && ((defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && ((defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && ((defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 6 && ((defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && ((defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 6 && ((defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && ((defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) linkfile3 Select the third gene to link (--link) perl defined $linkfile2 1 2 3 4 5 6 A given gene can only be linked once per run perl defined $linkfile3 && defined $linkfile21 && defined $linkfile22 && ($linkfile3 eq $linkfile21 || $linkfile3 eq $linkfile22) Sorry, the same gene cannot be linked twice to the same group perl defined $linkfile3 && ($linkfile3 eq $linkfile1 || $linkfile3 eq $linkfile2) Please enter the lowest gene number first perl defined $linkfile3 && $linkfile2 > $linkfile3 linkfile4 Select the fourth gene to link (--link) perl defined $linkfile3 1 2 3 4 5 6 Sorry, a given gene can only be linked once per run perl defined $linkfile4 && defined $linkfile21 && defined $linkfile22 && ($linkfile4 eq $linkfile21 || $linkfile4 eq $linkfile22) Sorry, the same gene cannot be linked twice to the same group perl defined $linkfile4 && ($linkfile4 eq $linkfile1 || $linkfile4 eq $linkfile2 || $linkfile4 eq $linkfile3) Please enter the lowest gene number first perl defined $linkfile4 && $linkfile3 > $linkfile4 linkfile5 Select the fifth gene to link (--link) perl defined $linkfile4 1 2 3 4 5 6 Sorry, a given gene can only be linked once per run perl defined $linkfile4 && defined $linkfile21 && defined $linkfile22 && ($linkfile4 eq $linkfile21 || $linkfile4 eq $linkfile22) Sorry, the same gene cannot be linked twice to the same group perl defined $linkfile4 && ($linkfile4 eq $linkfile1 || $linkfile4 eq $linkfile2 || $linkfile4 eq $linkfile3) Please enter the lowest gene number first perl defined $linkfile4 && $linkfile3 > $linkfile4 linkfile6 Select the sixth gene to link (--link) perl defined $linkfile5 1 2 3 4 5 6 Sorry, a given gene can only be linked once per run perl defined $linkfile4 && defined $linkfile21 && defined $linkfile22 && ($linkfile4 eq $linkfile21 || $linkfile4 eq $linkfile22) Sorry, the same gene cannot be linked twice to the same group perl defined $linkfile4 && ($linkfile4 eq $linkfile1 || $linkfile4 eq $linkfile2 || $linkfile4 eq $linkfile3) Please enter the lowest gene number first perl defined $linkfile4 && $linkfile3 > $linkfile4 Second_group_of_Genes_to_Link Select a second group of Genes to Link linkfile21 Select the first gene to link (--link) perl !defined $linkfile5 1 2 3 4 5 6 linkfile22 Select the second gene to link (--link) perl defined $linkfile21 1 2 3 4 5 6 Sorry, the same gene cannot be selected twice for linking perl defined $linkfile21 && defined $linkfile22 && ($linkfile21 eq $linkfile22) Sorry, the same gene cannot be selected twice for linking perl defined $linkfile23 && ($linkfile21 eq $linkfile23 || $linkfile22 eq $linkfile23) Sorry, the same gene cannot be selected twice for linking perl defined $linkfile24 && ($linkfile21 eq $linkfile24 || $linkfile22 eq $linkfile24 || $linkfile22 eq $linkfile24) Please select one more gene to link perl defined $linkfile21 && !defined $linkfile22 Please enter the lowest gene number first perl defined $linkfile22 && $linkfile21 > $linkfile22 linkfile23 Select the third gene to link (--link) perl defined $linkfile22 1 2 3 4 5 6 Please enter the lowest gene number first perl defined $linkfile23 && $linkfile22 > $linkfile23 Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && defined $datatype && defined $datatype_2 && ($datatype ne $datatype_2) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && defined $datatype && defined $datatype_3 && ($datatype ne $datatype_3) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && defined $datatype && defined $datatype_4 && ($datatype ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && defined $datatype && defined $datatype_5 && ($datatype ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && defined $datatype && defined $datatype_6 && ($datatype ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && defined $datatype_2 && defined $datatype_3 && ($datatype_2 ne $datatype_3) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && defined $datatype_2 && defined $datatype_4 && ($datatype_2 ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && defined $datatype_2 && defined $datatype_5 && ($datatype_2 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && defined $datatype_2 && defined $datatype_6 && ($datatype_2 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && defined $datatype_3 && defined $datatype_4 && ($datatype_3 ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && defined $datatype_3 && defined $datatype_5 && ($datatype_3 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && defined $datatype_3 && defined $datatype_6 && ($datatype_3 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && defined $datatype_4 && defined $datatype_5 && ($datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && defined $datatype_4 && defined $datatype_6 && ($datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 5 && $linkfile22 == 6 && defined $datatype_5 && defined $datatype_6 && ($datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && defined $datatype && defined $datatype_2 && defined $datatype_3 && ($datatype != $datatype_2 || $datatype != $datatype_3 || $datatype_2 != $datatype_3 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && defined $datatype && defined $datatype_2 && defined $datatype_4 && ($datatype != $datatype_2 || $datatype != $datatype_4 || $datatype_2 != $datatype_4 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_5 && ($datatype != $datatype_2 || $datatype != $datatype_5 || $datatype_2 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_3 && ($datatype != $datatype_2 || $datatype != $datatype_6 || $datatype_2 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && defined $datatype && defined $datatype_3 && defined $datatype_4 && ($datatype != $datatype_3 || $datatype != $datatype_4 || $datatype_3 != $datatype_4 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && defined $datatype && defined $datatype_3 && defined $datatype_5 && ($datatype != $datatype_3 || $datatype != $datatype_5 || $datatype_3 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && defined $datatype && defined $datatype_3 && defined $datatype_6 && ($datatype != $datatype_3 || $datatype != $datatype_6 || $datatype_3 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && defined $datatype && defined $datatype_4 && defined $datatype_5 && ($datatype != $datatype_4 || $datatype != $datatype_5 || $datatype_4 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && defined $datatype && defined $datatype_4 && defined $datatype_6 && ($datatype != $datatype_4 || $datatype != $datatype_6 || $datatype_4 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && defined $datatype && defined $datatype_5 && defined $datatype_6 && ($datatype != $datatype_5 || $datatype != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && ($datatype_2 != $datatype_3 || $datatype_2 != $datatype_4 || $datatype_3 != $datatype_4 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && ($datatype_2 != $datatype_3 || $datatype_2 != $datatype_5 || $datatype_3 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_6 && ($datatype_2 != $datatype_3 || $datatype_2 != $datatype_6 || $datatype_3 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && defined $datatype_2 && defined $datatype_4 && defined $datatype_5 && ($datatype_2 != $datatype_4 || $datatype_2 != $datatype_5 || $datatype_4 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && defined $datatype_2 && defined $datatype_4 && defined $datatype_6 && ($datatype_2 != $datatype_4 || $datatype_2 != $datatype_6 || $datatype_4 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && defined $datatype_2 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 != $datatype_5 || $datatype_2 != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype_3 != $datatype_4 || $datatype_3 != $datatype_5 || $datatype_4 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && defined $datatype_3 && defined $datatype_4 && defined $datatype_6 && ($datatype_3 != $datatype_4 || $datatype_3 != $datatype_6 || $datatype_4 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype_3 != $datatype_5 || $datatype_3 != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_4 != $datatype_5 || $datatype_4 != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && ($datatype ne $datatype_4 || $datatype_2 ne $datatype_4 || $datatype_3 ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_2 ne $datatype_5 || $datatype_3 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_4 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_2 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_4 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $datatype && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_3 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $datatype && defined $datatype_3 && defined $datatype_4 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype_2 ne $datatype_5 || $datatype_3 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype_2 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && defined $substitution_model && defined $substitution_model2 && ($substitution_model ne $substitution_model2) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && defined $substitution_model && defined $substitution_model3 && ($substitution_model ne $substitution_model3) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && defined $substitution_model && defined $substitution_model4 && ($substitution_model ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && defined $substitution_model && defined $substitution_model5 && ($substitution_model ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && defined $substitution_model && defined $substitution_model6 && ($substitution_model ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && defined $substitution_model2 && defined $substitution_model3 && ($substitution_model2 ne $substitution_model3) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && defined $substitution_model2 && defined $substitution_model4 && ($substitution_model2 ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && defined $substitution_model2 && defined $substitution_model5 && ($substitution_model2 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && defined $substitution_model2 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model3 ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model3 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model3 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 5 && $linkfile22 == 6 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model3 || $substitution_model2 != $substitution_model3 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model4 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model4 || $substitution_model2 != $substitution_model4 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model5 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model5 || $substitution_model2 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model6 || $substitution_model2 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model != $substitution_model3 || $substitution_model != $substitution_model4 || $substitution_model3 != $substitution_model4 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model != $substitution_model3 || $substitution_model != $substitution_model5 || $substitution_model3 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model != $substitution_model3 || $substitution_model != $substitution_model6 || $substitution_model3 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && defined $substitution_model && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model != $substitution_model4 || $substitution_model != $substitution_model5 || $substitution_model4 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && defined $substitution_model && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model != $substitution_model4 || $substitution_model != $substitution_model6 || $substitution_model4 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && defined $substitution_model && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model != $substitution_model5 || $substitution_model != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model2 != $substitution_model3 || $substitution_model2 != $substitution_model4 || $substitution_model3 != $substitution_model4 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model2 != $substitution_model3 || $substitution_model2 != $substitution_model5 || $substitution_model3 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model2 != $substitution_model3 || $substitution_model2 != $substitution_model6 || $substitution_model3 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model2 != $substitution_model4 || $substitution_model2 != $substitution_model5 || $substitution_model4 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model2 != $substitution_model4 || $substitution_model2 != $substitution_model6 || $substitution_model4 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && defined $substitution_model2 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 != $substitution_model5 || $substitution_model2 != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model3 != $substitution_model4 || $substitution_model3 != $substitution_model5 || $substitution_model4 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model3 != $substitution_model4 || $substitution_model3 != $substitution_model6 || $substitution_model4 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && defined $substitution_model3 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model3 != $substitution_model5 || $substitution_model3 != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model4 != $substitution_model5 || $substitution_model4 != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model ne $substitution_model4 || $substitution_model2 ne $substitution_model4 || $substitution_model3 ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model2 ne $substitution_model5 || $substitution_model3 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model2 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model3 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $substitution_model && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model2 ne $substitution_model5 || $substitution_model3 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) linkfile24 Select the fourth gene to link (--link) perl defined $linkfile23 1 2 3 4 5 6 Please enter the lowest gene number first perl defined $linkfile24 && $linkfile23 > $linkfile24 Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && defined $custom_model && defined $custom_model2 && ($custom_model ne $custom_model2) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && defined $custom_model && defined $custom_model3 && ($custom_model ne $custom_model3) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && defined $custom_model && defined $custom_model4 && ($custom_model ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && defined $custom_model && defined $custom_model5 && ($custom_model ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && defined $custom_model && defined $custom_model6 && ($custom_model ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && defined $custom_model2 && defined $custom_model3 && ($custom_model2 ne $custom_model3) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && defined $custom_model2 && defined $custom_model4 && ($custom_model2 ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && defined $custom_model2 && defined $custom_model5 && ($custom_model2 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && defined $custom_model2 && defined $custom_model6 && ($custom_model2 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && defined $custom_model3 && defined $custom_model4 && ($custom_model3 ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && defined $custom_model3 && defined $custom_model5 && ($custom_model3 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && defined $custom_model3 && defined $custom_model6 && ($custom_model3 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && defined $custom_model4 && defined $custom_model5 && ($custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && defined $custom_model4 && defined $custom_model6 && ($custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 5 && $linkfile22 == 6 && defined $custom_model5 && defined $custom_model6 && ($custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && ($custom_model != $custom_model2 || $custom_model != $custom_model3 || $custom_model2 != $custom_model3 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && defined $custom_model && defined $custom_model2 && defined $custom_model4 && ($custom_model != $custom_model2 || $custom_model != $custom_model4 || $custom_model2 != $custom_model4 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model5 && ($custom_model != $custom_model2 || $custom_model != $custom_model5 || $custom_model2 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && ($custom_model != $custom_model2 || $custom_model != $custom_model6 || $custom_model2 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && defined $custom_model && defined $custom_model3 && defined $custom_model4 && ($custom_model != $custom_model3 || $custom_model != $custom_model4 || $custom_model3 != $custom_model4 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && defined $custom_model && defined $custom_model3 && defined $custom_model5 && ($custom_model != $custom_model3 || $custom_model != $custom_model5 || $custom_model3 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && defined $custom_model && defined $custom_model3 && defined $custom_model6 && ($custom_model != $custom_model3 || $custom_model != $custom_model6 || $custom_model3 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && defined $custom_model && defined $custom_model4 && defined $custom_model5 && ($custom_model != $custom_model4 || $custom_model != $custom_model5 || $custom_model4 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && defined $custom_model && defined $custom_model4 && defined $custom_model6 && ($custom_model != $custom_model4 || $custom_model != $custom_model6 || $custom_model4 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && defined $custom_model && defined $custom_model5 && defined $custom_model6 && ($custom_model != $custom_model5 || $custom_model != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && ($custom_model2 != $custom_model3 || $custom_model2 != $custom_model4 || $custom_model3 != $custom_model4 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && defined $custom_model2 && defined $custom_model3 && defined $custom_model5 && ($custom_model2 != $custom_model3 || $custom_model2 != $custom_model5 || $custom_model3 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model6 && ($custom_model2 != $custom_model3 || $custom_model2 != $custom_model6 || $custom_model3 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && defined $custom_model2 && defined $custom_model4 && defined $custom_model5 && ($custom_model2 != $custom_model4 || $custom_model2 != $custom_model5 || $custom_model4 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && defined $custom_model2 && defined $custom_model4 && defined $custom_model6 && ($custom_model2 != $custom_model4 || $custom_model2 != $custom_model6 || $custom_model4 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && defined $custom_model2 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 != $custom_model5 || $custom_model2 != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model3 != $custom_model4 || $custom_model3 != $custom_model5 || $custom_model4 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model3 != $custom_model4 || $custom_model3 != $custom_model6 || $custom_model4 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && defined $custom_model3 && defined $custom_model5 && defined $custom_model6 && ($custom_model3 != $custom_model5 || $custom_model3 != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model4 != $custom_model5 || $custom_model4 != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && ($custom_model ne $custom_model4 || $custom_model2 ne $custom_model4 || $custom_model3 ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model2 ne $custom_model5 || $custom_model3 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model4 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model2 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $custom_model && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model3 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $custom_model && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $custom_model && defined $custom_model3 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $custom_model && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model2 ne $custom_model5 || $custom_model3 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $custom_model2 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && ((defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && ((defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && ((defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && ((defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && ((defined $gammarates41 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates46)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && ((defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && ((defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && ((defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && ((defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && ((defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && ((defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && ((defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && ((defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && ((defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && ((defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) )