IQ-Tree on ACCESS 1.6.12 - 3.0.1 Efficient phylogenomic software by maximum likelihood, run on XSEDE L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, and B.Q. Minh B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 37:1530-1534. https://doi.org/10.1093/molbev/msaa015 Phylogeny / Alignment iqtree_xsede iqtree_invoke16 perl $which_iqtree == 16 perl "iqtree_1.6.12_expanse" 0 iqtree_invoke212 perl $which_iqtree == 212 perl "iqtree2_2.1.2_expanse" 0 iqtree_invoke240 perl $which_iqtree == 301 perl "iqtree3_3.0.1.intel_expanse" 0 number_nodes212a 2 scheduler.conf perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns < 5000 && !defined $partition_file perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=12G\\n" . "threads_per_process=6\\n" number_nodes212c 2 scheduler.conf perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 4999 && $specify_numpatterns < 10000 && !defined $partition_file perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=24G\\n" . "threads_per_process=12\\n" number_nodes212d 2 scheduler.conf perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 9999 && $specify_numpatterns < 40000 && !defined $partition_file perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=48G\\n" . "threads_per_process=24\\n" number_nodes212e 2 scheduler.conf perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 39999 && $specify_numpatterns < 300000 && !defined $partition_file perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=96G\\n" . "threads_per_process=48\\n" number_nodes212f 2 scheduler.conf perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 299999 && !defined $partition_file perl "nodes=1\\n" . "node_exclusive=1\\n" . "mem=243G\\n" . "threads_per_process=128\\n" number_nodes212g 2 scheduler.conf perl $datatype ne "PROTEIN" && defined $partition_file && !$more_memory && !$more_memory2 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=11G\\n" . "threads_per_process=6\\n" number_nodes212h 2 scheduler.conf perl $more_memory && !$more_memory2 perl "nodes=1\\n" . "more_memory=4\\n" . "node_exclusive=0\\n" . "mem=96G\\n" . "threads_per_process=48\\n" number_nodes212i 2 scheduler.conf perl $more_memory2 perl "nodes=1\\n" . "node_exclusive=1\\n" . "mem=243G\\n" . "threads_per_process=128\\n" number_nodes212protx 2 scheduler.conf perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns < 1800 && !defined $partition_file perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=23G\\n" . "threads_per_process=12\\n" number_nodes212prota 2 scheduler.conf perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 1799 && $specify_numpatterns < 6000 && !defined $partition_file perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=46G\\n" . "threads_per_process=24\\n" number_nodes212protb 2 scheduler.conf perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 5999 && $specify_numpatterns < 40000 && !defined $partition_file perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=96G\\n" . "threads_per_process=48\\n" number_nodes212protc 2 scheduler.conf perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 39999 && !defined $partition_file perl "nodes=1\\n" . "node_exclusive=1\\n" . "mem=243G\\n" . "threads_per_process=128\\n" number_nodes212protd 2 scheduler.conf perl $datatype eq "PROTEIN" && defined $partition_file && !$more_memory && !$more_memory2 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=23G\\n" . "threads_per_process=12\\n" infile Input Alignment infile.txt infile_conditional perl !$mixed_sequence && !$specify_commandline perl "-s infile.txt" 1 runtime 90 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" As configured this job will run on 48 processors as configured; if it runs for the entire configured time it will be charged 48 x $runtime cpu hours perl $more_memory && !$more_memory2 As configured this job will require a full node. If it runs for the entire configured time, it will consume128 x $runtime cpu hours perl $more_memory2 The job will run on 6 processors as configured. If it runs for the entire configured time, it will consume 6 x $runtime cpu hours perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns < 5000 && !defined $partition_file The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hours perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 4999 && $specify_numpatterns < 10000 && !defined $partition_file The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x $runtime cpu hours perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 9999 && $specify_numpatterns < 40000 && !defined $partition_file The job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x $runtime cpu hours perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 39999 && $specify_numpatterns < 300000 && !defined $partition_file The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 299999 && !defined $partition_file WARNING: If your job runs for the full configured time, it will consume 3,000 - 6,000 cpu hours. Please consider if you want to do this. perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 299999 && $runtime >= 24 && $runtime <= 48 && !defined $partition_file WARNING: If your job runs for the full configured time, it will consume 6,000 - 9,000 cpu hours. Please consider if you want to do this. perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 299999 && $runtime > 48 && $runtime <= 72 && !defined $partition_file WARNING: If your job runs for the full configured time, it will consume 9,000 - 12,000 cpu hours. Please consider if you want to do this. perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 299999 && $runtime > 72 && $runtime <= 96 && !defined $partition_file WARNING: If your job runs for the full configured time, it will consume 12,000 - 15,000 cpu hours. Please consider if you want to do this. perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 299999 && $runtime > 96 && $runtime <= 120 && !defined $partition_file WARNING: If your job runs for the full configured time, it will consume 15,000 - 18,000 cpu hours. Please consider if you want to do this. perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 299999 && $runtime > 120 && $runtime <= 144 && !defined $partition_file WARNING: If your job runs for the full configured time, it will consume 18,000 - 21,000 cpu hours. Please consider if you want to do this. perl $datatype ne "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 299999 && $runtime > 144 && $runtime <= 168 && !defined $partition_file The job will run on 6 processors as configured. If it runs for the entire configured time, it will consume 6 x $runtime cpu hours perl $datatype ne "PROTEIN" && defined $partition_file && !$more_memory && !$more_memory2 The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hours perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns < 1800 && !defined $partition_file The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x $runtime cpu hours perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 1799 && $specify_numpatterns < 6000 && !defined $partition_file The job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x $runtime cpu hours perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 5999 && $specify_numpatterns < 40000 && !defined $partition_file The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 39999 && !defined $partition_file The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hours perl $datatype eq "PROTEIN" && !$more_memory && defined $partition_file WARNING: If your job runs for the full configured time, it will consume 3,000 - 6,000 cpu hours. Please consider if you want to do this. perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 39999 && $runtime >= 24 && $runtime <= 48 && !defined $partition_file WARNING: If your job runs for the full configured time, it will consume 6,000 - 9,000 cpu hours. Please consider if you want to do this. perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 39999 && $runtime > 48 && $runtime <= 72 && !defined $partition_file WARNING: If your job runs for the full configured time, it will consume 9,000 - 12,000 cpu hours. Please consider if you want to do this. perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 39999 && $runtime > 72 && $runtime <= 96 && !defined $partition_file WARNING: If your job runs for the full configured time, it will consume 12,000 - 15,000 cpu hours. Please consider if you want to do this. perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 39999 && $runtime > 96 && $runtime <= 120 && !defined $partition_file WARNING: If your job runs for the full configured time, it will consume 15,000 - 18,000 cpu hours. Please consider if you want to do this. perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 39999 && $runtime > 120 && $runtime <= 144 && !defined $partition_file WARNING: If your job runs for the full configured time, it will consume 18,000 - 21,000 cpu hours. Please consider if you want to do this. perl $datatype eq "PROTEIN" && !$more_memory && !$more_memory2 && $specify_numpatterns > 39999 && $runtime > 144 && $runtime <= 168 && !defined $partition_file Estimate the maximum time your job will need to run. We recommend testing 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. which_iqtree Which version do you want to run? 16 212 301 301 Please choose an IQ Tree version perl !defined $which_iqtree IQtree version 2.1.2 is much faster than other versions. We recommend using it if you can. perl $which_iqtree ne 212 specify_numpatterns How many patterns does your data set have? Please specify the number of patterns perl !defined $specify_numpatterns The number of patterns must be greater than zero perl $specify_numpatterns < 1 Please specify the number of patterns perl !defined $specify_numpatterns You can do a quick run, and the output log will tell you how many patterns are in your data set. more_memory I need more memory This option should only be used if analysis has run out of memory more_memory2 I need still more memory This option should only be used if analysis set with more memory has run out of memory specify_commandline I would like to specify my commandline in free text specify_commandline2 Please enter your commandline perl $specify_commandline perl "$specify_commandline2" Please enter your commandline perl $specify_commandline && !defined $specify_commandline2 specify_safe Safe likelihood kernel to avoid numerical underflow (-safe) perl !$specify_commandline perl ($value) ? "-safe":"" 29 datatype Specify your sequence type (-st) perl !$mixed_sequence DNA PROTEIN BINARY MORPH CODON NT2AA Please select the sequence type perl !defined $datatype && !$mixed_sequence 3 datatype2 perl $datatype eq "DNA" && !$specify_commandline perl "-st DNA" 3 datatype3 perl $datatype eq "PROTEIN" && !$specify_commandline perl "-st AA" 3 datatype4 perl $datatype eq "BIN" && !$specify_commandline perl "-st BIN" 3 datatype5 perl $datatype eq "MORPH" && !$specify_commandline perl "-st MORPH" 3 codon_type Specify your Codon type perl $datatype eq "CODON" && !$specify_commandline perl "-st $value" CODON1 CODON2 CODON3 CODON4 CODON5 CODON6 CODON9 CODON10 CODON11 CODON12 CODON13 CODON14 CODON16 CODON21 CODON22 CODON23 CODON24 CODON25 CODON1 Please specify your Codon code type perl $datatype eq "CODON" && !defined $codon_type && !$specify_commandline 2 nt2aa_type Specify your translation table perl $datatype eq "NT2AA" && !$specify_commandline perl "-st $value" NT2AA1 NT2AA2 NT2AA3 NT2AA4 NT2AA5 NT2AA6 NT2AA9 NT2AA10 NT2AA11 NT2AA12 NT2AA13 NT2AA14 NT2AA16 NT2AA21 NT2AA22 NT2AA23 NT2AA24 NT2AA25 NT2AA1 Please select your translation table type perl $datatype eq "NT2AA" && !defined nt2aa_type && !$specify_commandline 2 starting_tree Specify a starting (or other) tree file (-t) treefile.tre 4 Note that your treefile will be named treefile.tre; your command line must include -t treefile.tre perl defined $starting_tree && $specify_commandline starting_tree2 Specify a starting (or other) tree file (-t) perl !$specify_commandline && defined $starting_tree perl "-t treefile.tre" 4 use_nj Use a NJ starting tree (-t BIONJ) perl !defined $starting_tree && !$specify_commandline perl ($value) ? "-t BIONJ":"" Sorry, you cannot choose both a random and a NJ starting tree perl $use_nj && $use_random 4 use_random Use a Random starting tree (-t RANDOM) perl !defined $starting_tree && !$specify_commandline perl ($value) ? "-t RANDOM":"" 4 specify_outgroup Specify the outgroup (-o) perl !$specify_commandline && !$specify_commandline perl (defined $value) ? "-o $value":"" 4 specify_prefix Specify the prefix for output files (-pre'/ --prefix) perl !$specify_commandline output 30 specify_prefix1 perl defined $specify_prefix && $which_iqtree < 20 perl "-pre $specify_prefix" 29 specify_prefix2 perl defined $specify_prefix && $which_iqtree > 200 perl "--prefix $specify_prefix" 29 specify_seed Specify a seed (-seed) perl !$specify_commandline perl (defined $value) ? "-seed $value":"" 4 quartet_options Quartet Options specify_quartets Quartets to be randomly drawn (-lmap) perl !$specify_commandline ALL specify_quartet 4 specify_quartetall perl $specify_quartets eq "ALL" perl "-lmap ALL" 4 specify_quartetnum Specify number of quartets perl $specify_quartets eq "specify_quartet" perl defined $value ? "-lmap $value":"" Please specify the number of quartets perl $specify_quartets eq "specify_quartet" && !defined $specify_quartetnum 4 specify_quartetset Select a NEXUS file specifying taxon clusters (-lmclust) clusters.nex 4 Note that your clusters file will be named clusters.nex; your command line must include -lmclust clusters.nex perl defined $specify_quartetset && $specify_commandline specify_quartetset2 perl defined $specify_quartetsets && !$specify_commandline perl "-lmclust clusters.nex" 4 specify_numparsquartets Specify number of parsimony-based sCF quartets (--scf) perl $which_iqtree > 200 && !$specify_commandline perl (defined $value) ? "--scf $value":"" The authors recommend at least 100 quartets for stable values perl (defined $specify_numparsquartets) && $specify_numparsquartets < 100 specify_numlikquartets Specify number of likelihood-based ssCF quartets (--scfl) perl $which_iqtree > 200 && !$specify_commandline perl "--scfl $value" Sorry, you cant specify both --scf and --scfl perl defined $specify_numlikquartets && defined $specify_numparsquartets The authors recommend at least 100 quartets for stable values perl (defined $specify_numlikquartets) && $specify_numlikquartets < 100 write_quartets Write quartets to a file perl defined $specify_quartets && !$specify_commandline perl $write_quartets ? "-wql":"" 4 partition_options Partition Options partition_file Please select your partition file 10 partition_file.txt Your partition file will be named partition_file.txt, you must include this name in your commandline perl defined $partition_file && $specify_commandline nexus_partition_file My partitions are specified in a Nexus file perl defined $partition_file partition_type Please select your partition type perl defined $partition_file && !$specify_commandline -q -spp -sp Please specify your partition type perl !defined $partition_type && defined $partition_file && !$specify_commandline partition_command2 perl defined $partition_type && $which_iqtree < 200 && !$specify_commandline perl "$partition_type partition_file.txt" 2 partition_command3 perl defined $partition_type && $which_iqtree > 200 && $partition_type eq "-spp" && !$specify_commandline perl "-p partition_file.txt" 2 partition_command4 perl defined $partition_type && $which_iqtree > 200 && $partition_type eq "-sp" && !$specify_commandline perl "-Q partition_file.txt" 2 partition_command5 perl defined $partition_type && $which_iqtree > 200 && $partition_type eq "-q" && !$specify_commandline perl "-q partition_file.txt" 2 mixed_sequence I want to use multiple alignment files for a partitioned analysis perl $nexus_partition_file 0 num_mixedsequences How many alignment files in your partitioned analysis perl $mixed_sequence 2 3 4 5 datatype2_file Select the second alignment file (alignment2.phy) perl $num_mixedsequences > 1 alignment2.phy Your second alignment file will be named alignment2.phy, use this name to call the file from your nexus partition file perl defined $datatype2_file && $specify_commandline datatype3_file Select the file with your third datatype (alignment3.phy) perl $num_mixedsequences > 2 alignment3.phy Your third alignment file will be named alignment3.phy, use this name to call the file from your nexus partition file perl defined $datatype3_file && $specify_commandline datatype4_file Select the file with your fourth datatype (alignment4.phy) perl $num_mixedsequences > 3 alignment4.phy Your fourth alignment file will be named alignment4.phy, use this name to call the file from your nexus partition file perl defined $datatype4_file && $specify_commandline datatype5_file Select the file with your fifth datatype (alignment5.phy) perl $num_mixedsequences > 4 alignment5.phy Your fifth alignment file will be named alignment5.phy, use this name to call the file from your nexus partition file perl defined $datatype5_file && $specify_commandline model_selection Automatic Model Selection specify_model Test for the best model (-m TEST) perl !$specify_commandline TESTONLY TEST TESTNEWONLY TESTNEW TESTMERGEONLY TESTMERGE TESTNEWMERGEONLY TESTNEWMERGE perl (defined $value) ? "-m $value$specify_liemarkov":"" 4 The default model (e.g.,HKY+Ffor DNA,LGfor protein data) may not fit well to thedata. Therefore, IQ-TREE allows to automatically determine the best-fit model via a series of-m TEST...options: specify_liemarkov Specify a Lie Markov Option perl !$specify_commandline +LM +LMRY +LMWS +LMMK +LMSS select_rcluster Specify the relaxed clustering algorithm to use (-rcluster) perl !$specify_commandline -rcluster -rclusterf -rcluster-max Use this option to specify the percentage for the relaxed clustering algorithm (Lanfear et al., 2014). This is similar to -*rcluster-percent option of PartitionFinder. For example, with -rcluster 10 only the top 10% partition schemes are considered to save computations. specify_rclusterval Specify the percentage or max partition pairs for relaxed clustering algorithm perl !$specify_commandline perl (defined $value) ? "$select_rcluster $value":"" 4 Please specify the rcluster algorithm perl defined $specify_rclusterval && !defined $select_rcluster Please specify the percentage or max partition pairs for the rcluster algorithm perl !defined $specify_rclusterval && defined $select_rcluster Use this option to specify the percentage for the relaxed clustering algorithm (Lanfear et al., 2014). This is similar to -*rcluster-percent option of PartitionFinder. For example, with -rcluster 10 only the top 10% partition schemes are considered to save computations. specify_basemodels Specify names of the base models or program (-mset) perl !$specify_commandline perl (defined $value) ? "-mset $value":"" 4 For -mset, specify the name of a program (raxml, phyml or mrbayes) to restrict to only those models supported by the specified program. Alternatively, one can specify a comma-separated list of base models. For example, -mset WAG,LG,JTT will restrict model selection to WAG, LG, and JTT instead of all 18 AA models to save computations. specify_aamodels Specify nuclear, mitochondrial, chloroplast or viral (-msub, protein) perl $datatype eq "PROTEIN" && !$specify_commandline nuclear mitochondrial chloroplast viral perl (defined $value) ? "-msub $value":"" 4 specify_freqtypes Specify a comma-separated list of frequency types for model selection (-mfreq) perl !$specify_commandline perl (defined $value) ? "-mfreq $value":"" 4 specify_ratehettypes Specify a comma-separated list of rate heterogeneity types for model selection (-mrate) perl !$specify_commandline perl (defined $value) ? "-mrate $value":"" 4 specify_mincat Specify minimum number of categories for FreeRate model (-cmin) perl !$specify_commandline perl (defined $value) ? "-cmin $value":"" 4 specify_maxcat perl !$specify_commandline Specify maximum number of categories for FreeRate model (-cmax) perl (defined $value) ? "-cmax $value":"" 4 specify_merit Specify either AIC, AICc or BIC for the optimality criterion (-merit) perl !$specify_commandline perl (defined $value) ? "-merit $value":"" 4 specify_fulltreesearch Turn on full tree search for each model considered, to obtain more accurate result. (-mtree) perl !$specify_commandline perl ($value) ? "-mtree":"" 4 specify_addlmodels Specify a comma-separated list of mixture models to additionally consider for model selection. (-madd) perl !$specify_commandline perl (defined $value) ? "-madd $value":"" 4 specify_nexusmodelfile Specify a Nexus Model file. (-mdef) modelfile.nex 4 Your Nexus model file will be named modelfile.nex, use this name in your command line to access the nexus model file perl defined $specify_nexusmodelfile && $specify_commandline specify_nexusmodelfile2 perl defined $specify_nexusmodelfile && !$specify_commandline perl "-mdef modelfile.nex" 4 specify_subst Specify Substitution Models freetextmodel Specify any model using free text (-m) perl !$specify_commandline Sorry, you cant specify a DNA model and use the free text entry perl defined $freetextmodel && defined $specify_dnamodel 4 dnamodel_string perl $datatype eq "DNA" && !$specify_commandline perl (defined $specify_dnamodel) ? "-m $specify_dnamodel$specify_modelfreq$specify_modelrate$asc_bias":"" 4 model_string2 perl !$specify_commandline perl (defined $freetextmodel) ? "-m $freetextmodel":"" 4 specify_dnamodel Specify a DNA model (-m ) perl $datatype eq "DNA" && !$specify_commandline JC69 F81 K80 HKY TN93 TNe K81 K81u TPM2 TPM2u TPM3 TPM3u TIM TIMe TIM2 TIM2e TIM3 TIM3e TVM TVMe SYM GTR 4 aamodel_string perl $datatype eq "PROTEIN" && !$specify_commandline perl (defined $specify_protmodel) ? "-m $specify_protmodel$specify_modelfreq$specify_modelrate":"" 4 specify_protmodel Specify a Protein model (-m ) perl ($datatype eq "PROTEIN" || $datatype eq "NT2AA") && !$specify_commandline BLOSUM62 cpREV Dayhoff DCMut FLU HIVb HIVw JTT JTTDCMut LG mtART mtMAM mtREV mtZOA mtMet mtVer mtInv Poisson PMB rtREV VT WAG EAL ELM Q.LG Q.pfam Q.pfam_gb Q.bird Q.mammal Q.insect Q.plant Q.yeast Sorry, you cant specify a protein model and use the free text entry perl defined $freetextmodel && defined $specify_protmodel && !$specify_commandline 3 specify_protmixture Specify a Protein Profile mixture perl ($datatype eq "PROTEIN" || $datatype eq "NT2AA") && defined $specify_protmodel && !$specify_commandline +C10 +C20 +C30 +C40 +C50 +C60 +EX2 +EX3 +EHO +UL2 +UL3 +EX_EHO +LG4M +LG4X +CF4 3 guide_tree Specify a guide tree file for PMSF analysis (-ft) guidetree.tre perl ($specify_protmodel eq "C10" || $specify_protmodel eq "C20" || $specify_protmodel eq "C30" || $specify_protmodel eq "C40" || $specify_protmodel eq "C50" || $specify_protmodel eq "C60") Note that your quidetree file will be named guidetree.tre; your command line must include -ft guidetree.tre perl defined $guide_tree && $specify_commandline 4 guide_tree2 perl ($specify_protmodel eq "C10" || $specify_protmodel eq "C20" || $specify_protmodel eq "C30" || $specify_protmodel eq "C40" || $specify_protmodel eq "C50" || $specify_protmodel eq "C60") && !$specify_commandline perl "-ft guidetree.tre" 4 frequency_file Specify a frequency file for PMSF analysis (-fs) sitefreq.file perl ($specify_protmodel eq "C10" || $specify_protmodel eq "C20" || $specify_protmodel eq "C30" || $specify_protmodel eq "C40" || $specify_protmodel eq "C50" || $specify_protmodel eq "C60") 4 Note that your sitefreq file will be named sitefreq.file; your command line must include -fs sitefreq.file perl defined $frequency_file && $specify_commandline frequency_file2 perl ($specify_protmodel eq "C10" || $specify_protmodel eq "C20" || $specify_protmodel eq "C30" || $specify_protmodel eq "C40" || $specify_protmodel eq "C50" || $specify_protmodel eq "C60") && !$specify_commandline perl "-fs sitefreq.file" 4 max_posteriormode Switch to posterior maximum mode for obtaining site-specific profiles (-fmax) perl ($specify_protmodel eq "C10" || $specify_protmodel eq "C20" || $specify_protmodel eq "C30" || $specify_protmodel eq "C40" || $specify_protmodel eq "C50" || $specify_protmodel eq "C60") && !$specify_commandline perl $max_posteriormode ? "-fmax":"" 4 binmodel_string perl $datatype eq "BIN" && !$specify_commandline perl (defined $specify_binmodel) ? "-m $specify_binmodel$specify_modelfreq$specify_modelrate":"" 4 specify_binmodel Specify a Binary/Morphological model (-m ) perl ($datatype eq "BIN" || $datatype eq "MORPH") && !$specify_commandline JC2 GTR2 MK ORDERED Sorry, you cant specify a BIN model and use the free text entry perl defined $freetextmodel && defined $specify_binmodel Sorry, you cant specify use a MK or Ordered for BIN data perl $datatype eq "BIN" && ($specify_binmodel eq "MK" || $specify_binmodel eq "ORDERED") Sorry, you cant specify use a JC2 or GTR2 for morpohological data perl $datatype eq "MORPH" && ($specify_binmodel eq "JC2" || $specify_binmodel eq "GTR2") 4 codonmodel_string perl $datatype eq "CODON" && !$specify_commandline perl (defined $specify_codonmodel) ? "-m $specify_codonmodel$specify_modelfreq$specify_modelrate":"" 4 specify_codonmodel Specify a Codon model (-m ) perl $datatype eq "CODON" && !$specify_commandline MG MGK MG1KTS MG1KTV MG2K GY GY0K GY1KTS GY1KTV GY2K KOSI07 ECMrest SCHN05 GY Sorry, you cant specify a CODON model and use the free text entry perl defined $freetextmodel && defined $specify_codonmodel specify_modelfreq Specify model frequency perl !$specify_commandline +F +FO +FQ +F1x4 +F3x4 optimize_weights Turn on optimizing weights of mixture models (-mwopt) perl !$specify_commandline perl $value ? "-mwopt":"" 4 specify_modelrate Specify rate heterogeneity perl !$specify_commandline +I +G +I+G +R +I+R asc_bias Correct for Ascertainment bias (+ASC) perl !$specify_commandline +ASC This is useful for binary/morphological datasets that only contain variable sites (the identical morphological features are usually not included in the alignments, hence you need to correct for this, see, e.g., http://sysbio.oxfordjournals.org/content/50/6/913.short).For DNA data this option might be useful when you analyze alignments of SNPs that also don't contain constant sites. Note that, for mathematical and numerical reasons you can not apply an ascertainment bias correction to datasets or partitions that contain constant sites. gamma_shape Specify the Gamma shape parameter (-a) perl !$specify_commandline perl (defined $value ) ? "-a $value":"" 4 The gamma shape parameter must be greater than 0 perl defined $gamma_shape && $gamma_shape <= 0 median_approximation Perform the median approximation for Gamma rate heterogeneity (-gmedian) perl !$specify_commandline perl ($value ) ? "-gmedian":"" 4 Perform the median approximation for Gamma rate heterogeneity instead of the default mean approximation (Yang, 1994) invariable_sites Specify the proportion of invariable sites (-i) perl !$specify_commandline perl (defined $value ) ? "-i $value":"" 4 thorough_estimation Perform more thorough estimation for +I+G model parameters (--opt-gamma-inv) perl !$specify_commandline perl ($value ) ? "--opt-gamma-inv":"" 4 tree_search_params Tree Search Parameters slower_NNI Turn on more thorough and slower NNI search (-allnni) perl !$specify_commandline perl ($value ) ? "-allnni":"" 20 Turn on more thorough and slower NNI search. It means that IQ-TREE will consider all possible NNIs instead of only those in the vicinity of previously applied NNIs. DEFAULT: OFF no_mlpairwise Avoid computing ML pairwise distances and BIONJ tree (-djc) perl !$specify_commandline perl ($value ) ? "-djc":"" 4 Avoid computing ML pairwise distances and BIONJ tree. use_fasttreesearch Turn on the fast tree search mode (-fast) perl !$specify_commandline perl ($value ) ? "-fast":"" 4 Avoid computing ML pairwise distances and BIONJ tree. constraint_file Specify a topological constraint tree file in NEWICK format (-g) constraintfile.txt 4 Note that your constraint tree file will be named constraintfile.txt; your command line must include -g constraintfile.txt perl defined $constraint_file && $specify_commandline Specify a topological in NEWICK format. The constraint tree can be a multifurcating tree and need not include all taxa. constraint_file2 perl defined $constraint_file && !$specify_commandline perl "-g constraintfile.txt" 4 num_parstrees Specify number of initial parsimony trees (-ninit) perl !$specify_commandline perl (defined $value ) ? "-ninit $value":"" 4 Specify number of initial parsimony trees. DEFAULT: 100. Here the PLL library (Flouri et al., 2015) is used, which implements the randomized stepwise addition and parsimony subtree pruning and regafting (SPR). num_tostop Number of iterations to stop (-n) perl !$specify_commandline perl (defined $value ) ? "-n $value":"" 5 Sorry, the -n parameter cannot be used with Ultrafast Bootstrapping perl (defined $value) && $bootstrap_type eq "bb" Specify number of iterations to stop. This option overrides -nstop criterion. Use -n 0 to only estimate model parameters on an initial parsimony tree and ignore a full tree search to save time num_topparstrees Specify number of top initial parsimony trees (-ntop) perl !$specify_commandline perl (defined $value ) ? "-ntop $value":"" 7 Specify number of top initial parsimony trees to optimize with ML nearest neighbor interchange (NNI) search to initialize the candidate set. DEFAULT: 20 num_besttrees Number of trees in the candidate set to maintain (-nbest) perl !$specify_commandline perl (defined $value ) ? "-nbest $value":"" 6 Specify number of trees in the candidate set to maintain during ML tree search. DEFAULT: 5 num_unsucctostop Number of unsuccessful iterations to stop (-nstop) perl !$specify_commandline perl (defined $value ) ? "-nstop $value":"" 8 Specify number of unsuccessful iterations to stop. DEFAULT: 100 perturb_strength Perturbation strength (between 0 and 1) (-pers) perl !$specify_commandline perl (defined $value ) ? "-pers $value":"" 8 Specify perturbation strength (between 0 and 1) for randomized NNI. DEFAULT: 0.5 specify_radius SPR radius for the initial search (-sprrad) perl !$specify_commandline 9 6 Specify SPR radius for the initial parsimony tree search. DEFAULT: 6 specify_radiusval20 perl $which_iqtree > 19 && defined $specify_radius perl "--sprrad $specify_radius" 10 specify_radiusval16 perl $which_iqtree < 19 && defined $specify_radius perl "-sprrad $specify_radius" 10 ultrafast_search_params Bootstrap Search Parameters bootstrap_type Bootstrap Type perl !$specify_commandline bb b bo bc 11 bootstrap_typeh1 perl $bootstrap_type eq bb && $which_iqtree < 212 perl "-bb $num_bootreps" 12 bootstrap_typeh2 perl $bootstrap_type eq bb && $which_iqtree > 16 perl "-B $num_bootreps" 13 bootstrap_typeh3 perl defined $bootstrap_type && $bootstrap_type ne "bb" perl "-$bootstrap_type $num_bootreps" 14 num_bootreps Specify number of bootstrap replicates (>=1000 for ultrafast) perl defined $bootstrap_type Please enter a number of bootstraps perl defined $bootstrap_type && !defined $num_bootreps For ultrafast, the value of bootstraps must be greater than or equal to 1,000 perl $bootstrap_type eq "bb" && $num_bootreps < 1000 -b: Specify number of bootstrap replicates (recommended >=100; for ultrafast (-bb) >=1000). This will perform both bootstrap and analysis on original alignment and provide a consensus tree. -bc Like -b but omit analysis on original alignment. -bo Like -b but only perform bootstrap analysis (no analysis on original alignment and no consensus tree). max_iters Specify maximum number of iterations to stop. (-nm) perl defined $bootstrap_type perl (defined $value ) ? "-nm $value":"" Specify maximum number of iterations to stop. DEFAULT: 1000 iter_interval Iteration interval checking for UFBoot convergence (-nstep) perl defined $bootstrap_type perl (defined $value ) ? "-nstep $value":"" Step size must be a multiple of 2 perl defined $iter_interval && ((($iter_interval) % 2) != 0) Step size must be at least 10 perl defined $iter_interval && $iter_interval < 10 Specify iteration interval checking for UFBoot convergence. DEFAULT: every 100 iterations cc_ufboot Minimum correlation coefficient for UFBoot convergence criterion (-bcor) perl defined $bootstrap_type perl (defined $value ) ? "-bcor $value":"" Specify minimum correlation coefficient for UFBoot convergence criterion. DEFAULT: 0.99 specify_tiebreaker SPR radius for the initial search (-beps) perl defined $bootstrap_type perl (defined $value ) ? "-beps $value":"" Specify a small epsilon to break tie in RELL evaluation for bootstrap trees. DEFAULT: 0.5 use_bnni Use bnni to reduce overestimating support (-bnni) perl $bootstrap_type eq "bb" perl ($value) ? "-bnni" : "" 1 part_resample Resampling strategies for partitioned analysis (-bspec/-bsam) perl defined $partition_file && !$specify_commandline GENE GENESITE Specify the resampling strategies for partitioned analysis. By default, IQ-TREE resamples alignment sites within partitions. With -bspec GENE IQ-TREE will resample partitions. With -bspec GENESITE IQ-TREE will resample partitions and then resample sites within resampled partitions (Gadagkar et al., 2005). part_resample1 perl $which_iqtree < 19 && !$use_bnni && !$specify_commandline perl (defined $part_resample) ? "-bspec $part_resample":"" part_resample2 perl $which_iqtree < 19 && $use_bnni && !$specify_commandline perl (defined $part_resample) ? "-bspec $part_resample -keep_empty_seq":"" part_resample3 perl $which_iqtree > 200 && !$use_bnni && !$specify_commandline perl (defined $part_resample ) ? "-bsam $part_resample":"" part_resample4 perl $which_iqtree > 200 && $use_bnni && !$specify_commandline perl (defined $part_resample) ? "-bsam $part_resample -keep_empty_seq":"" write_boottrees Turn on writing bootstrap trees to .ufboot file (-wbt) perl defined $bootstrap_type perl ($value) ? "-wbt":"" 0 Turn on writing bootstrap trees to .ufboot file. DEFAULT: OFF write_boottrees1 Turn on writing bootstrap trees with branch lengths (-wbtl) perl defined $bootstrap_type perl ($value) ? "-wbtl":"" 0 Turn on writing bootstrap trees with branch lengths (-wbt1) DEFAULT: OFF symmetry_tests Symmetry Tests use_symmtest Run symmetry test(s) perl !$specify_commandline 0 specify_symtest Symmetry Test (--symtest) perl $use_symmtest symtest symtest-remove-bad symtest-remove-good symtest-keep-zero symtest "--symtest" symtest-remove-bad "--symtest-remove-bad" symtest-remove-good "--symtest-remove-good" symtest-keep-zero "--symtest-keep-zero" 91 specify_symtype When removing partitions, use perl !$specify_commandline pval MAR INT perl ($value ne $vdef) ? "--symtest-type $value":"" pval 92 specify_pval Specify a Symmetry p-value other than 0.05 perl !$specify_commandline perl defined $value ? "--symtest-pval $specify_pval":"" Please enter a pval for symmetry perl !defined $specify_pval && $specify_symtest eq "symtest-pval" 92 IQ-TREE provides three matched-pairs tests of symmetry (Naser-Khdour et al., 2019) to test the two assumptions of stationarity and homogeneity. iqtree2 -s example.phy -p example.nex --symtest will perform the three tests of symmetry on every partition of the alignment and print the result into a .symtest.csv file. You can configure the analysis to judge by pval, intval, or marval. You can set the p-value for whichever you choose to adjust the cutoff between good and bad partitions. single_branchtest Single Branch Tests sh_test SH-Like Test (-alrt) perl $bootstrap_type ne "b" && $bootstrap_type ne "bo" && $bootstrap_type ne "bc" && !$specify_commandline perl ($value) ? "-alrt $num_replicates":"" 6 parametrical_test Run the parametricaLRT test (-alrt 0) perl $bootstrap_type ne "b" && $bootstrap_type ne "bo" && $bootstrap_type ne "bc" && !$specify_commandline perl ($value) ? "-alrt 0":"" 6 abayes_test Approximate Bayes test (-abayes) perl $bootstrap_type ne "b" && $bootstrap_type ne "bo" && $bootstrap_type ne "bc" && !$specify_commandline perl ($value) ? "-abayes":"" 6 lbp_test Fast local bootstrap probability (-lbp) perl $bootstrap_type ne "b" && $bootstrap_type ne "bo" && $bootstrap_type ne "bc" && !$specify_commandline perl ($value) ? "-lbp $num_replicates":"" 6 num_replicates Specify number of replicates (1000 or more) perl $sh_test || $lbp_test The value of replicates must be greater than or equal to 1,000 perl defined $num_replicates && $num_replicates < 1000 && $lbp_test The value of replicates must be greater than or equal to 1,000 for the SH- test perl defined $num_replicates && $sh_test && $num_replicates < 1000 Please enter a value for number of replicates perl !defined $num_replicates && ($sh_test || $lbp_test) ancestral_reconstruction Ancestral State Reconstruction write_ancestralseqs Write ancestral sequences to .statefile (-asr) perl $which_iqtree > 19 && !$specify_commandline perl $value ? "-asr":"" specify_ancestralthresh Specify minimum threshold of posterior probability for best ancestral state (-asr-min) perl $which_iqtree > 19 && !$specify_commandline perl $value ? "-asr-min $value":"" specify_ancestraltree Specify a user-defined tree to determine ancestral sequences (-te) perl $which_iqtree > 19 ancestralseqs.tre Note that your ancestral sequences file will be named ancestralseqs.tre; your command line must include -te ancestralseqs.tre perl defined $specify_ancestraltree && $specify_commandline specify_ancestraltree2 perl defined $specify_ancestraltree && !$specify_commandline perl "-te ancestralseqs.tre" tree_topology Tree Topology Tests specify_treefile Specify a file containing a set of trees (-z) treesfile.tre Note that your tree file will be named treesfile.tre; your command line must include -z treesfile.tre perl defined $specify_treefile && $specify_commandline specify_treefile2 perl defined $specify_treefile && !$specify_commandline perl "-z treesfile.tre" num_rell Specify the number of RELL replicates (-zb) perl !$specify_commandline perl (defined $value) ? "-zb $value":"" Sorry, the number of RELL replicates cannot be less than 1,000 perl defined $num_rell && $num_rell < 1000 && !$specify_commandline -zb Specify the number of RELL (Kishino et al., 1990) replicates (>=1000) to perform several tree topology tests for all trees passed via -z. The tests include bootstrap proportion (BP), KH test (Kishino and Hasegawa, 1989), SH test (Shimodaira and Hasegawa, 1999) and expected likelihood weights (ELW) (Strimmer and Rambaut, 2002). weighted_tests Perform the weighted-KH and weighted-SH tests (-zw) perl defined $num_rell perl ($value) ? "-zw":"" unbiased_test Perform the approximately unbiased (AU) test perl !$specify_commandline perl ($value) ? "-au":"" Note that you have to specify the number of replicates for the AU test via-zb perl $unbiased_test && !defined $num_rell estimate_parsetreeonly Only estimate model parameters on an initial parsimony tree (-n 0) perl defined $num_rell perl ($value) ? "-n 0":"" Only estimate model parameters on an initial parsimony tree and ignorea full tree search to save time. fixed_usertree Specify a fixed user tree to estimate model parameters (-te) fixed_usertree.tre Note that your fixed user tree file will be named fixed_usertree.tre; your command line must include -te fixed_usertree.tre perl defined $fixed_usertree && $specify_commandline -te Specify a fixed user tree to estimate model parameters. Thus it behaves like -n 0 but uses a user-defined tree instead of parsimony tree. fixed_usertree2 perl defined $fixed_usertree && !$specify_commandline perl "-te fixed_usertree.tre" consensus_tree Consensus Trees tree_file1 Specify a file containing a set of trees treefile1.tre Note that your set of trees file will be named treefile1.tre; your command line must include -t treefile1.tre perl defined $tree_file1 && $specify_commandline tree_file2 perl defined $tree_file1 && !$specify_commandline perl "-t treefile1.tre" compute_consensustree Compute consensus tree of the trees passed via -t (-con) perl defined $tree_file1 && !$specify_commandline perl ($value) ? "-con":"" -con Compute consensus tree of the trees passed via -t. Resulting consensus tree is written to .contree file. compute_consensusnetwork Compute consensus network of the trees passed via -t (-net) perl defined $tree_file1 && !$specify_commandline perl ($value) ? "-net":"" min_threshold Specify a minimum threshold between 0 and 1 (-minsup) perl defined $tree_file1 && !$specify_commandline perl ($value) ? "-minsup $min_threshold":"" The value for -minsup must be between 0 and 1 perl $min_threshold < 0 || $min_threshold > 1 && !$specify_commandline burnin_value Specify a burn-in (-bi) perl defined $tree_file1 && !$specify_commandline perl (defined $value) ? "-bi $value":"" target_treefile Specify an input “target” tree file (-sup) targetfile.tre Note that your target tree file will be named targetfile.tre; your command line must include -sup targetfile.tre perl defined $target_treefile && $specify_commandline -sup Specify an input “target” tree file. That means, support values are first extracted from the trees passed via -t, and then mapped onto the target tree. Resulting tree with assigned support values is written to .suptree file. This option is useful to map and compare support values from different approaches onto a single tree. target_treefile2 perl defined $target_treefile && !$specify_commandline perl "-sup targetfile.tre" set_scalefactor Set the scaling factor of support values for -sup option (-scale) perl defined $target_treefile perl (defined $value) ? "-scale $value":"" -suptag Specify name of a node in -sup target tree. The corresponding node of .suptree will then be assigned with IDs of trees where this node appears. Special option -suptag ALL will assign such IDs for all nodes of the target tree. set_precision Set the precision of support values for -sup option (-prec) perl defined $target_treefile && !$specify_commandline perl (defined $value) ? "-prec $value":"" nodetarget_treefile Specify name of a node in -sup target tree (-suptag) perl defined $target_treefile && !$specify_commandline perl (defined $value) ? "-suptag $value":"" robinsons_fouldsdist Computing Robinson's Foulds distances tree_file2 Specify a second set of trees for RF distances (-rf) treefile2.tre Note that your second set of trees file will be named treefile2.tre; your command line must include -rf treefile2.tre perl defined $tree_file2 && $specify_commandline tree_file2b perl defined $tree_file2 && !$specify_commandline perl "-rf treefile2.tre" compute_rfdistances_all Compute all-to-all RF distances between all trees passed via -t (-rf_all) perl defined $tree_file1 && !$specify_commandline perl ($value) ? "-rf_all":"" compute_rfdistances_adj Compute RF distances between adjacent trees passed via -t (-rf_adj) perl defined $tree_file1 && !$specify_commandline perl ($value) ? "-rf_adj":"" specify_rfdistancestree Select file of adjacent trees to pass via -t rfdistance.tre Note that your set of adjacent trees file will be named rfdistance.tre; your command line must include -t rfdistance.tre perl defined $specify_rfdistancestree && $specify_commandline specify_rfdistancestree2 perl defined $specify_rfdistancestree && !$specify_commandline perl "-t rfdistance.tre" generate_randomtrees Generate Random Trees (Only) num_taxa Specify number of taxa for the tree (-r) perl !$specify_commandline Please choose a random tree model perl !defined $choose_randomtype && defined $num_taxa If you select a random tree option, the program will create a random tree and exit without further action perl defined $num_taxa choose_randomtype Specify a model for the random trees perl defined $num_taxa && !$specify_commandline -r -ru -rcat -rbal -rcsg perl (defined $value) ? "$value $num_taxa $specify_treefilename":"" specify_brlengths Specify minimum, mean and maximum branch lengths of the random tree DEFAULT:-rlen 0.001 0.1 0.999 perl defined $num_taxa && !$specify_commandline perl (defined $value) ? "-rlen $value":"" Specify three numbers: minimum, mean and maximum branch lengths of the random tree. specify_treefilename Specify a name for your random tree file (we recommend a name with .tree) perl defined $num_taxa && !$specify_commandline Please specify a name for your random tree file output perl defined $num_taxa && !defined $specify_treefilename Sorry, you cant specify random trees and provide a starting tree perl defined $tree_file1 && defined $specify_treefilename Specify a name for the random tree output. Consider adding the .tree extension cf_options Concordance Factor Options (Version 2 only) partition_modelfile2 Choose file that specifies the model selection (-S) perl $which_iqtree > 200 alignment_file.txt You cannot specify a -S file and a -p partition file perl defined $partition_modelfile2 && defined $partition_file Note that your set of model selection file will be named alignment_file.txt; your command line must include -S alignment_file.txt perl defined $partition_modelfile2 && $specify_commandline partition_modelfile2b perl defined $partition_modelfile2 && !$specify_commandline perl "-S alignment_file.txt" name_outfiles Specify a prefix for the output files (--prefix) perl !$specify_commandline perl (defined $value) ? "--prefix $value":"" You have entered two different prefixes. Please remove one. perl defined $name_outfiles && defined $specify_prefix partition_tfile Choose a reference tree file (coalescent/reconciliation approach) for gCF (-t) perl $which_iqtree > 200 concat.treefile Note that your reference tree file for gCF will be named concat.treefile.tre; your command line must include -t concat.treefile perl defined $partition_tfile && $specify_commandline Note that -t accepts any reference tree (e.g., by coalescent/reconciliation approach) and --gcf accepts any set of trees (e.g. locus trees and bootstrap trees), which may contain a subset of taxa from the reference tree. IQ-Tree will write three files: concord.cf.tree: Newick tree with gCF assigned for each internal branch of the reference tree. If the reference tree already has some branch label (such as bootstrap support in this case), gCF will be appended to the existing label separated by a /. concord.cf.branch: Newick tree with internal branch IDs. concord.cf.stat: A tab-separated table with gCF and gDF (gene discordance factor) for every internal branch (rows of the table). The ID column can be linked with concord.cf.branch file. This file can be read in R to do some plotting. partition_tfile2 perl $which_iqtree > 200 && defined $partition_tfile && !$specify_commandline perl "-t concat.treefile" setoftrees_file Choose a set of trees for gCF (-gcf) perl $which_iqtree > 200 loci.treefile Note that your set of trees for gCF will be named loci.treefile; your command line must include -gcf loci.treefile perl defined $setoftrees_file && $specify_commandline setoftrees_file2 perl defined $setoftrees_file && !$specify_commandline perl "--gcf loci.treefile" dating_options Dating Options (Version 2 only) specify_datefile Choose a file that specifies dates (--date) perl $which_iqtree > 200 date_file.txt Note that your date file will be named date_file.txt; your command line must include --date date_file.txt perl defined $specify_datefile && $specify_commandline specify_datefile2 perl $which_iqtree > 200 && defined $specify_datefile && !$specify_commandline perl "--date date_file.txt" extract_datefile Automatically extract dates from taxon Names (--date TAXNAME) perl defined $specify_datefile && !$specify_commandline perl ($value) ? "--date TAXNAME":"" specify_datetip Specify tip dates as a real number or YYYY-MM-DD (--date-tip) perl $which_iqtree > 200 && !$specify_commandline perl (defined $value) ? "--date-tip $value":"" specify_rootdate Specify root date as a real number or YYYY-MM-DD (--date-root) perl $which_iqtree > 200 && !$specify_commandline perl (defined $value) ? "--date-root $value":"" specify_datetreefile Load and fix this tree topology (-te) perl $which_iqtree > 200 treetopology.txt Note that your fixed tree topology file will be named treetopology.txt; your command line must include -te treetopology.txt perl defined $specify_datetreefile && $specify_commandline specify_datetreefile2 perl defined $specify_datetreefile && !$specify_commandline perl "--date treetopology.txt" specify_resampleint Resample branch lengths to infer the confidence interval (--date-ci) perl $which_iqtree > 200 && !$specify_commandline perl ($value > 0 ) ? "--date-ci $value":"" specify_outlierthresh z-score threshold to detect outliers (--date-outlier) perl $which_iqtree > 200 && !$specify_commandline perl (defined $value) ? "--date-outlier $value":"" misc_options Miscellaneous Options print_sitestats Print alignment site statistics to.alninfofile (-alninfo) perl !$specify_commandline perl ($value) ? "-alninfo":"" 90 fix_branchlengths Fix branch lengths of tree passed via -te. (-blfix) branchlengths_tree Provide a tree to fix branch lengths (-te) perl $fix_branchlengths fixbranchlengths.tre Please provide a tree for fixing branch lengths perl $fix_branchlengths && !defined $branchlengths_tree Note that your fixed tree topology file will be named fixbranchlengths.tre; your command line must include --te fixbranchlengths.tre perl defined $branchlengths_tree && $specify_commandline branchlengths_tree2 perl defined $branchlengths_tree && !$specify_commandline perl "-blfix -te fixbranchlengths.tre" specify_minbranchlength Specify minimum branch length. (-blmin) perl !$specify_commandline perl ($value) ? "-blmin":"" specify_maxbranchlength Specify maximum branch length. (-blmax) perl !$specify_commandline perl ($value) ? "-blmax":"" write_locally_optimal Turn on writing all locally optimal trees (-wt) perl ($value) ? "-wt":"" fix_brlengths Turn on fixing branch lengths of tree passed via -t or -te (-fixbr) perl !$specify_commandline && (defined $tree_file1 || defined $fixed_usertree) perl ($value) ? "-fixbr":"" -fixbr Turn on fixing branch lengths of tree passed via -t or -te. This is useful to evaluate the log-likelihood of an input tree with fixed tolopogy and branch lengths. per_sitefile Write per-site rates to .rate file (-wsr) perl !$specify_commandline perl ($value ) ? "-wsr":"" per_sitewslfile Write site log-liklihoods to .sitelh file (-wsl) perl !$specify_commandline perl ($value ) ? "-wsl":"" per_sitewslrfile Write site log-likelihoods per rate category (-wslr) perl !$specify_commandline perl ($value ) ? "-wslr":"" per_sitewslmfile Write site log-likelihoods per mixture class (-wslm) perl !$specify_commandline perl ($value ) ? "-wslm":"" per_sitewslmrfile Write site log-likelihoods per mixture+rate class (-wslmr) perl !$specify_commandline perl ($value ) ? "-wslmr":"" per_sitewspmfile Write site probabilities per mixture class (-wspm) perl !$specify_commandline perl ($value ) ? "-wspm":"" per_sitewsprfile Write site probabilities per rate category (-wspr) perl !$specify_commandline perl ($value ) ? "-wspr":"" per_sitewspmrfile Write site probabilities per rate category (-wspmr) perl !$specify_commandline perl ($value ) ? "-wspmr":"" per_sitewplfile Write partition log-likelihoods to .partlh file (-wpl) perl !$specify_commandline perl ($value ) ? "-wpl":"" write_sitelikelihoods Write log-likelihoods in TREE-PUZZLE format (-wsl) perl !$specify_commandline perl ($value) ? "-wsl":"" Turn on writing site log-likelihoods to .sitelh file in TREE-PUZZLE format. Such file can then be passed on to CONSEL for further tree tests. DEFAULT: OFF write_loglikelihoods Write log-likelihoods per rate category (-wslg) perl !$specify_commandline perl ($value) ? "-wslg":"" Turn on writing site log-likelihoods per rate category. DEFAULT: OFF list_csintegers Specify a list of comma-separated integer numbers (-fconst) integerfile.csv Note that your list of comma-separated integer number file will be named integerfile.csv; your command line must include -fconst integerfile.csv perl defined $list_csintegers && $specify_commandline Specify a list of comma-separated integer numbers. The number of entries should be equal to the number of states in the model (e.g. 4 for DNA and 20 for protein). IQ-TREE will then add a number of constant sites accordingly. For example, -fconst 10,20,15,40 will add 10 constant sites of all A, 20 constant sites of all C, 15 constant sites of all G and 40 constant sites of all T into the alignment. list_csintegers2 perl defined $list_csintegers && !$specify_commandline perl "-fconst integerfile.csv" results *