ModelTest-NG on ACCESS 0.1.7 Statistical selection of best-fit models of nucleotide and protein substitution, run on XSEDE Diego Darriba, David Posada, Alexandros Stamatakis, and Tomas Flouris Darriba D, Posada D., Alexandros Stamatakis, and Tomas Flouris at https://github.com/ddarriba/modeltest Phylogeny / Alignment modeltest_ng_xsede jmodeltest2_invoke perl "" 0 number_nodes 2 scheduler.conf perl $datatype eq "DNA" perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=42G\\n" . "cpus-per-task=22\\n" . "threads_per_process=22\\n" number_nodes2 2 scheduler.conf perl $datatype eq "PROTEIN" perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=73G\\n" . "cpus-per-task=38\\n" . "threads_per_process=38\\n" infile Input Alignment infile.phy perl "-i infile.phy" 1 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" The job will run on 22 processors as configured. If it runs for the entire configured time, it will consume 22 x $runtime cpu hours perl $datatype eq "DNA" The job will run on 38 processors as configured. If it runs for the entire configured time, it will consume 38 x $runtime cpu hours perl $datatype eq "PROTEIN" Estimate the maximum time your job will need to run. We recommend testimg initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. datatype Specify your datatype DNA PROTEIN perl ($value eq "PROTEIN") ? "-d aa":"" 3 user_fixedtree Select a User-defined fixed tree for likelihood calculations (-u) userfixedtree.tre perl "-u userfixedtree.tre" 8 asc_bias Ascertainment bias algorithm (-a) perl $set_heterogeneity eq "u" lewis felsenstein stamatakis perl defined $value ? "-a $value":"" To use Felsenstein, must specify the number of invariant sites in a partition file perl $asc_bias eq "felsenstein" && !defined $user_partitionfile To use Stamatakis, you must specify the invariant sites composition in a partition file perl $asc_bias eq "stamatakis" && !defined $user_partitionfile 25 Felsenstein requires number of invariant sites Stamatakis Leach et al. (2015) requires invariant sites composition name_output Specify the name of your output file (-o) perl (defined $value) ? "-o $value":"" 3 specify_topology Specify topology type (-t) perl ($value) ? "-t $value":"" ml mp fixed-ml-jc fixed-ml-gtr random user mp 2 set_heterogeneity Select the candidate model's rate heterogeneity (-h) u i g f perl " -h $value" Please set the model rate heterogeneity perl !defined $set_heterogeneity 5 user_partitionfile Select a user-defined partition file (-q) partition.txt perl defined $value ? "-q partition.txt":"" 8 specify_seed Specify a seed value (-r) perl defined $value ? "-r $value":"" 8 choose_models DNA Candidate Models specify_frequencies Select the candidate models frequencies (-f) perl $datatype eq "DNA" perl (defined $value) ? "-f $value":"" e f 13 model_lists Enter the DNA candidate model matrices separated by commas (-m) perl $datatype eq "DNA" JC, HKY, TrN, TPM1, TPM2, TPM3, TIM1, TIM2, TIM3, TVM, GTR, perl (defined $value) ? "-m $value":"" Please select a model, subscheme, or template perl $datatype eq "DNA" && !defined $model_lists && !defined $set_subschemes && !defined $template_tool ' ' 7 allowed values for dna: JC HKY TrN TPM1 TPM2 TPM3 TIM1 TIM2 TIM3 TVM GTR set_subschemes Set the number of substitution schemes (-s) perl $datatype eq "DNA" 3 5 7 11 203 perl " -s $value" 11 5 This flag sets the number of substitution schemes. 3 = JC/F81 K80/HKY SYM/GTR; 5 = JC/F81, K80/HKY, TrNef/TrN, TPM1/TPM1uf, SYM/GTR 7 = JC/F81, K80/HKY, TrNef/TrN, TPM1/TPM1uf, TIM1ef/TIM1, TVMef/TVM, SYM/GTR; 11 = all named models; 203 = All possible GTR submatrices template_tool Set DNA candidate models according to a specified tool perl $datatype eq "DNA" perl (defined $value) ? "-T $value":"" raxml phyml mrbayes paup Sorry the options -T, -m and -s are mutually exclusive perl defined $template_tool && defined $set_subschemes || defined $template_tool && defined $model_lists || defined $set_subschemes && defined $model_lists 18 choose_models Protein Candidate Models specify_protfrequencies Select the candidate protein models frequencies (-f) perl $datatype eq "PROTEIN" perl (defined $value) ? "-f $value":"" e f 13 protmodel_lists Enter the Amino Acid candidate model matrices separated by commas (-m) perl $datatype eq "PROTEIN" DAYHOFF, LG, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, MTART, MTZOA, PMB, HIVB, HIVW, JTTDCMUT, FLU, STMTRE, perl (defined $value) ? "-m $value":"" Please select a model, subscheme or template perl $datatype && !defined $protmodel_lists && !defined $set_subschemes && !defined $protemplate_tool ' ' 7 Allowed values for protein: DAYHOFF LG DCMUT JTT MTREV WAG RTREV CPREV VT BLOSUM62 MTMAM MTART MTZOA PMB HIVB HIVW JTTDCMUT FLU STMTREV set_protsubschemes Set the number of protein substitution schemes (-s) perl $datatype eq "PROTEIN" 3 5 7 11 203 perl " -s $value" 11 5 This flag sets the number of substitution schemes. 3 = JC/F81 K80/HKY SYM/GTR; 5 = JC/F81, K80/HKY, TrNef/TrN, TPM1/TPM1uf, SYM/GTR 7 = JC/F81, K80/HKY, TrNef/TrN, TPM1/TPM1uf, TIM1ef/TIM1, TVMef/TVM, SYM/GTR; 11 = all named models; 203 = All possible GTR submatrices protemplate_tool Set amino acid candidate models according to a specified tool perl $datatype eq "PROTEIN" perl (defined $value) ? "-T $value":"" raxml phyml mrbayes paup Sorry the options -T, -m and -s are mutually exclusive perl defined $protemplate_tool && defined $set_protsubschemes || defined $protemplate_tool && defined $protmodel_lists || defined $set_protsubschemes && defined $protmodel_lists 18 other_options Other Options set_epsilon Sets the model optimization epsilon. (-eps) perl defined $value ? "--eps $value":"" 10 set_tolerance Set the parameter optimization tolerance (--tol) perl defined $value ? "--tol $value":"" 10 criteria_1 Force frequencies smoothing (--smooth-frequencies) perl ($value) ? "--smooth-frequencies":"" disable_patterncompression Disables pattern compression (-H) perl ($value) ? "-H":"" 13 all_results *