IQ-Tree on XSEDE 2.1.11 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 iqtree2_xsede iqtree_invoke10 perl $which_iqtree < 20 perl "iqtree_1.6.10_comet" 0 iqtree_invoke205 perl $which_iqtree eq 205 perl "iqtree2_2.0.5_comet" 0 iqtree_invoke206 perl $which_iqtree eq 206 perl "iqtree2_2.0.6_comet" 0 iqtree_invoke211 perl $which_iqtree eq 211 perl "iqtree2_2.1.1_comet" 0 number_nodes1 2 scheduler.conf perl $specify_runtype == 1 && !$specify_autocores && $specify_numparts < 13 && $which_iqtree < 20 perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=12\\n" number_nodes1b 2 scheduler.conf perl $specify_runtype == 1 && $specify_autocores && $which_iqtree < 20 perl "nodes=1\\n" . "node_exclusive=1\\n" . "threads_per_process=24\\n" number_nodes1d 2 scheduler.conf perl $specify_runtype == 1 && !$specify_autocores && $specify_numparts > 12 && $which_iqtree < 20 perl "nodes=1\\n" . "node_exclusive=1\\n" . "threads_per_process=24\\n" number_nodes2 2 scheduler.conf perl $specify_runtype == 2 && $specify_numparts < 13 && $specify_numparts > 1 && $which_iqtree < 20 perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=12\\n" number_nodes2b 2 scheduler.conf perl $specify_runtype == 2 && $specify_numparts == 1 && $specify_mem < 60 && $which_iqtree < 20 perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=12\\n" number_nodes2c 2 scheduler.conf perl $specify_runtype == 2 && $specify_numparts == 1 && $specify_mem > 60 && $which_iqtree < 20 perl "nodes=1\\n" . "node_exclusive=1\\n" . "threads_per_process=24\\n" number_nodes2d 2 scheduler.conf perl $specify_runtype == 2 && $specify_numparts > 12 && $which_iqtree < 20 perl "nodes=1\\n" . "node_exclusive=1\\n" . "threads_per_process=24\\n" number_nodes205a 2 scheduler.conf perl $sequence_type ne "AA" && $specify_numparts < 2 && $specify_numpatterns < 2000 && $specify_mem < 121 && $which_iqtree > 20 perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=6\\n" number_nodes205b 2 scheduler.conf perl $sequence_type ne "AA" && $specify_numparts < 2 && $specify_numpatterns > 1999 && $specify_numpatterns < 6000 && $specify_mem < 121 && $which_iqtree > 20 perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=12\\n" number_nodes205c 2 scheduler.conf perl $sequence_type ne "AA" && $specify_numparts < 2 && $specify_numpatterns > 5999 && $specify_mem < 121 && $which_iqtree > 20 perl "nodes=1\\n" . "node_exclusive=1\\n" . "threads_per_process=24\\n" number_nodes205d 2 scheduler.conf perl $sequence_type ne "AA" && $specify_numparts > 1 && $specify_numpatterns < 10000 && $specify_mem < 121 && $which_iqtree > 20 perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=6\\n" number_nodes205e 2 scheduler.conf perl $sequence_type ne "AA" && $specify_numparts > 1 && $specify_numpatterns > 9999 && $specify_mem < 121 && $which_iqtree > 20 perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=12\\n" number_nodes205prot1 2 scheduler.conf perl $sequence_type eq "AA" && $specify_numpatterns < 3000 && $specify_mem < 121 && $which_iqtree > 20 perl "nodes=1\\n" . "node_exclusive=1\\n" . "threads_per_process=24\\n" number_nodes205prot2 2 scheduler.conf perl $sequence_type eq "AA" && $specify_numpatterns > 2999 && $specify_mem < 121 && $which_iqtree > 20 perl "nodes=1\\n" . "node_exclusive=1\\n" . "threads_per_process=24\\n" number_nodes205himem 2 scheduler.conf perl $specify_mem > 120 && $which_iqtree > 20 perl "threads_per_process=24\\n" . "large_data=1\\n" . "request_mem=540G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" infile Input Alignment infile.txt infile_conditional perl !$mixed_sequence perl "-s infile.txt" 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 For high memory jobs, the maximum hours to run is 48 hours perl $runtime > 48 && $specify_mem > 120 perl "runhours=$value\\n" 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 $specify_runtype == 1 && $which_iqtree < 20 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 $specify_runtype == 2 && $specify_numparts > 12 && $which_iqtree < 20 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 $specify_runtype == 2 && $specify_numparts == 1 && $specify_mem > 60 && $which_iqtree < 20 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 $specify_runtype == 2 && $specify_numparts < 13 && !defined $specify_mem && $which_iqtree < 20 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 $specify_runtype == 2 && $specify_numparts == 1 && defined $specify_mem && $specify_mem < 60 && $which_iqtree < 20 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 $sequence_type ne "AA" && $specify_numparts < 2 && $specify_numpatterns < 2000 && $specify_mem < 121 && $which_iqtree > 20 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 $sequence_type ne "AA" && $specify_numparts < 2 && $specify_numpatterns > 1999 && $specify_numpatterns < 6000 && $specify_mem < 121 && $which_iqtree > 20 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 $sequence_type ne "AA" && $specify_numparts < 2 && $specify_numpatterns > 5999 && $specify_mem < 121 && $which_iqtree > 20 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 $sequence_type ne "AA" && $specify_numparts > 1 && $specify_numpatterns < 10000 && $specify_mem < 121 && $which_iqtree > 20 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 $sequence_type ne "AA" && $specify_numparts > 1 && $specify_numpatterns > 9999 && $specify_mem < 121 && $which_iqtree > 20 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 $sequence_type eq "AA" && $specify_numpatterns < 3000 && $specify_mem < 121 && $which_iqtree > 20 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 $sequence_type eq "AA" && $specify_numpatterns > 2999 && $specify_mem < 121 && $which_iqtree > 20 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 $specify_mem > 120 && $which_iqtree > 20 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 16 205 206 211 211 specify_numpatterns How many patterns does your data set have? Please specify the number of patterns perl !defined $specify_numpatterns The number of partitions 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. specify_numparts How many partitions does your data set have Please specify the number of partitions perl !defined $specify_numparts The number of partitions must be greater than zero perl $specify_numparts < 1 Please specify the number of partitions perl !defined $specify_numparts specify_mem Memory required (in GB) The run will not complete if -mem is greater than 120 GB, please contact us for help. perl $specify_mem > 120 && $which_iqtree < 20 You can do a quick run, and the output log will tell you how much memory is required specify_safe Safe likelihood kernel to avoid numerical underflow (-safe) perl ($value) ? "-safe":"" specify_twelvecores perl $specify_runtype == 1 && !$specify_autocores && $which_iqtree < 20 perl "-nt 12" 3 specify_autocores Automatically select number of threads perl $specify_runtype == 1 && $which_iqtree < 20 perl ($value) ? "-nt AUTO":"" 3 specify_cores3 perl $specify_runtype == 2 && $which_iqtree < 20 perl "-nt AUTO" 3 specify_cores4 perl $specify_runtype == 2 && defined $specify_mem && !defined $partition_file perl "-mem $specify_mem$specify_g" 4 specify_g perl $specify_runtype == 2 && defined $specify_mem G specify_runtype Select the kind of run you need 1 2 Please specify whether the run is for Tree inference or Model Selection perl !defined $value 3 sequence_type Specify your sequence type (-st) perl !$mixed_sequence perl ($value ne "CODON" && $value ne "NT2AA") ? "-st $value":"" DNA AA BIN MORPH CODON NT2AA DNA 1 codon_type Specify your Codon type perl $sequence_type eq "CODON" perl "-st $value" CODON1 CODON2 CODON3 CODON4 CODON5 CODON6 CODON9 CODON10 CODON11 CODON12 CODON13 CODON14 CODON16 CODON21 CODON22 CODON23 CODON24 CODON25 CODON1 3 nt2aa_type Specify your translation table perl $sequence_type eq "NT2AA" perl "-st $value" NT2AA1 NT2AA2 NT2AA3 NT2AA4 NT2AA5 NT2AA6 NT2AA9 NT2AA10 NT2AA11 NT2AA12 NT2AA13 NT2AA14 NT2AA16 NT2AA21 NT2AA22 NT2AA23 NT2AA24 NT2AA25 NT2AA1 3 starting_tree Specify a starting (or other) tree file (-t) treefile.tre perl (defined $value) ? "-t treefile.tre":"" 3 use_nj Use a NJ starting tree (-t BIONJ) perl !defined $starting_tree perl ($value) ? "-t BIONJ":"" Sorry, you cannot choose both a random and a NJ starting tree perl $use_nj && $use_random 3 use_random Use a Random starting tree (-t RANDOM) perl !defined $starting_tree perl ($value) ? "-t RANDOM":"" 3 specify_outgroup Specify the outgroup (-o) perl (defined $value) ? "-o $value":"" 3 specify_prefix Specify the prefix for output files (-pre'/ --prefix) output 3 specify_prefix1 perl defined $specify_prefix && $which_iqtree < 20 perl "-pre $specify_prefix" 3 specify_prefix2 perl defined $specify_prefix && $which_iqtree > 20 perl "--prefix $specify_prefix" 3 specify_seed Specify the seed (-seed) perl (defined $value) ? "-seed $value":"" 3 specify_quartets Specify number of quartets (-lmap) perl (defined $value) ? "-lmap $value":"" 3 partition_options Partition Options partition_type Please select your partition type (V 1.x) perl $specify_numparts > 1 && $which_iqtree < 20 -q -spp -sp Please specify the partition type perl !defined $partition_modelfile && !defined $partition_type && $specify_numparts > 1 You have selected partition files for two different kinds of analysis. Please remove one. perl defined $partition_modelfile && defined $partition_file partition_type2 Please select your partition type (V 2.*) perl $specify_numparts > 1 && $which_iqtree > 200 -q -p -Q Please specify the partition type perl !defined $partition_modelfile && !defined $partition_type2 && $specify_numparts > 1 You have selected partition files for two different kinds of analysis. Please remove one. perl defined $partition_modelfile && defined $partition_file partition_file Please select your partition file perl defined $partition_type || defined $partition_type2 partition_file.txt Please select your partition file perl $specify_numparts > 1 && !defined $partition_file partition_command perl defined $partition_type perl (defined $partition_type) ? "$partition_type partition_file.txt":"" 6 partition_command2 perl defined $partition_type2 perl (defined $partition_type2) ? "$partition_type2 partition_file.txt":"" 6 mixed_sequence I want to mix data types in a partitioned analysis perl defined $partition_type || defined $partition_type2 0 num_mixedsequences How many data types (files) in your partitioned analysis perl $mixed_sequence 2 3 4 5 datatype2_file Select the file with your second datatype (partition_datatype2.phy) perl $num_mixedsequences > 1 partition_datatype2.phy datatype3_file Select the file with your third datatype (partition_datatype3.phy) perl $num_mixedsequences > 2 partition_datatype3.phy datatype4_file Select the file with your fourth datatype (partition_datatype4.phy) perl $num_mixedsequences > 3 partition_datatype4.phy datatype5_file Select the file with your fifth datatype (partition_datatype5.phy) perl $num_mixedsequences > 4 partition_datatype5.phy model_selection Automatic Model Selection specify_model Test for the best model (-m TEST) TESTONLY TEST TESTNEWONLY TESTNEW TESTMERGEONLY TESTMERGE TESTNEWMERGEONLY TESTNEWMERGE perl (defined $value) ? "-m $value$specify_liemarkov":"" You must specify a partition file to use the MERGE options perl ($specify_model eq "TESTMERGEONLY" || $specify_model eq "TESTMERGE" || $specify_model eq "TESTNEWMERGEONLY" || $specify_model eq "TESTNEWMERGE") && !defined $partition_file 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: 3 specify_liemarkov Specify a Lie Markov Option +LM +LMRY +LMWS +LMMK +LMSS select_rcluster Specify the relaxed clustering algorithm to use (-rcluster) -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 (defined $value) ? "$select_rcluster $value":"" 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 (defined $value) ? "-mset $value":"" 3 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 $sequence_type eq "AA" && $specify_runtype == 1 nuclear mitochondrial chloroplast viral perl (defined $value) ? "-msub $value":"" 3 specify_freqtypes Specify a comma-separated list of frequency types for model selection (-mfreq) perl $specify_runtype == 1 perl (defined $value) ? "-mfreq $value":"" 3 specify_ratehettypes Specify a comma-separated list of rate heterogeneity types for model selection (-mrate) perl $specify_runtype == 1 perl (defined $value) ? "-mrate $value":"" 3 specify_mincat Specify minimum number of categories for FreeRate model (-cmin) perl $specify_runtype == 1 perl (defined $value) ? "-cmin $value":"" 3 specify_maxcat perl $specify_runtype == 1 Specify maximum number of categories for FreeRate model (-cmax) perl (defined $value) ? "-cmax $value":"" 3 specify_merit Specify either AIC, AICc or BIC for the optimality criterion (-merit) perl $specify_runtype == 1 perl (defined $value) ? "-merit $value":"" 3 specify_fulltreesearch Turn on full tree search for each model considered, to obtain more accurate result. (-mtree) perl $specify_runtype == 1 perl ($value) ? "-mtree":"" 3 specify_addlmodels Specify a comma-separated list of mixture models to additionally consider for model selection. (-madd) perl $specify_runtype == 1 perl (defined $value) ? "-madd $value":"" 3 specify_nexusmodelfile Specify a Nexus Model file. (-mdef) perl $specify_runtype == 1 modelfile.nex perl (defined $value) ? "-mdef modelfile.nex":"" 3 specify_subst Specify Substitution Models freetextmodel Specify any model using free text (-m) perl $specify_runtype == 2 Sorry, you cant specify a DNA model and use the free text entry perl defined $freetextmodel && defined $specify_dnamodel 3 dnamodel_string perl $sequence_type eq "DNA" && $specify_runtype == 2 perl (defined $specify_dnamodel) ? "-m $specify_dnamodel$specify_modelfreq$specify_modelrate$asc_bias":"" model_string2 perl $specify_runtype == 2 perl (defined $freetextmodel) ? "-m $freetextmodel":"" specify_dnamodel Specify a DNA model (-m ) perl $sequence_type eq "DNA" && $specify_runtype == 2 JC69 F81 K80 HKY TN93 TNe K81 K81u TPM2 TPM2u TPM3 TPM3u TIM TIMe TIM2 TIM2e TIM3 TIM3e TVM TVMe SYM GTR 3 Sorry, you cant specify a DNA model and run a model test perl defined $specify_model && defined $value aamodel_string perl $sequence_type eq "AA" && $specify_runtype == 2 perl (defined $specify_protmodel) ? "-m $specify_protmodel$specify_protmixture$specify_modelfreq$specify_modelrate":"" specify_protmodel Specify a Protein model (-m ) perl ($sequence_type eq "AA" || $sequence_type eq "NT2AA") && $specify_runtype == 2 BLOSUM62 cpREV Dayhoff DCMut FLU HIVb HIVw JTT JTTDCMut LG mtART mtMAM mtREV mtZOA mtMet mtVer mtInv Poisson PMB rtREV VT WAG C10 C20 C30 C40 C50 C60 EX2 EX3 EHO UL2 UL3 EX_EHO LG4M LG4X CF4 Sorry, you cant specify a protein model and use the free text entry perl defined $freetextmodel && defined $specify_protmodel 3 specify_protmixture Specify a Protein Profile mixture perl ($sequence_type eq "AA" || $sequence_type eq "NT2AA") && $specify_runtype == 2 && defined $specify_protmodel +C10 +C20 +C30 +C40 +C50 +C60 +EX2 +EX3 +EHO +UL2 +UL3 +EX_EHO +LG4M +LG4X +CF4 3 guide_tree Specify a guide tree file for PMSF analysis (-ft) guidetree.tre perl ($specify_protmixture eq "C10" || $specify_protmixture eq "C20" || $specify_protmixture eq "C30" || $specify_protmixture eq "C40" || $specify_protmixture eq "C50" || $specify_protmixture eq "C60" || $specify_protmodel eq "C10" || $specify_protmodel eq "C20" || $specify_protmodel eq "C30" || $specify_protmodel eq "C40" || $specify_protmodel eq "C50" || $specify_protmodel eq "C60") perl (defined $value) ? "-ft guidetree.tre":"" 3 frequency_file Specify a frequency file for PMSF analysis (-fs) sitefreq.file perl ($specify_protmixture eq "C10" || $specify_protmixture eq "C20" || $specify_protmixture eq "C30" || $specify_protmixture eq "C40" || $specify_protmixture eq "C50" || $specify_protmixture eq "C60" || $specify_protmodel eq "C10" || $specify_protmodel eq "C20" || $specify_protmodel eq "C30" || $specify_protmodel eq "C40" || $specify_protmodel eq "C50" || $specify_protmodel eq "C60") perl (defined $value) ? "-fs sitefreq.file":"" 3 max_posteriormode Switch to posterior maximum mode for obtaining site-specific profiles (-fmax) sitefreq.file perl ($specify_protmixture eq "C10" || $specify_protmixture eq "C20" || $specify_protmixture eq "C30" || $specify_protmixture eq "C40" || $specify_protmixture eq "C50" || $specify_protmixture eq "C60" || $specify_protmodel eq "C10" || $specify_protmodel eq "C20" || $specify_protmodel eq "C30" || $specify_protmodel eq "C40" || $specify_protmodel eq "C50" || $specify_protmodel eq "C60") perl (defined $value) ? "-fmax":"" 3 binmodel_string perl $sequence_type eq "BIN" && $specify_runtype == 2 perl (defined $specify_binmodel) ? "-m $specify_binmodel$specify_modelfreq$specify_modelrate":"" specify_binmodel Specify a Binary/Morphological model (-m ) perl ($sequence_type eq "BIN" || $sequence_type eq "MORPH") && $specify_runtype == 2 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 $sequence_type eq "BIN" && ($specify_binmodel eq "MK" || $specify_binmodel eq "ORDERED") Sorry, you cant specify use a JC2 or GTR2 for morpohological data perl $sequence_type eq "MORPH" && ($specify_binmodel eq "JC2" || $specify_binmodel eq "GTR2") 3 codonmodel_string perl $sequence_type eq "CODON" && $specify_runtype == 2 perl (defined $specify_codonmodel) ? "-m $specify_codonmodel$specify_modelfreq$specify_modelrate":"" specify_codonmodel Specify a Codon model (-m ) perl $sequence_type eq "CODON" && $specify_runtype == 2 MG MGK MG1KTS MG1KTV MG2K GY GY1KTS GY1KTV GY2K KOSI07 ECMrest SCHN05 Sorry, you cant specify a CODON model and use the free text entry perl defined $freetextmodel && defined $specify_codonmodel 3 specify_modelfreq Specify model frequency perl $specify_runtype == 2 +F +FO +FQ +F1x4 +F3x4 3 optimize_weights Turn on optimizing weights of mixture models (-mwopt) perl $value ? "-mwopt":"" 3 specify_modelrate Specify rate heterogeneity perl $specify_runtype == 2 +I +G +I+G +R +I+R 3 asc_bias Correct for Ascertainment bias (+ASC) perl $specify_runtype == 2 +ASC 2 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_runtype == 2 perl (defined $value ) ? "-a $value":"" 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 $specify_runtype == 2 perl ($value ) ? "-gmedian":"" 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_runtype == 2 perl (defined $value ) ? "-i $value":"" thorough_estimation Perform more thorough estimation for +I+G model parameters (--opt-gamma-inv) perl $specify_runtype == 2 perl ($value ) ? "--opt-gamma-inv":"" tree_search_params Tree Search Parameters slower_NNI Turn on more thorough and slower NNI search (-allnni) perl $specify_runtype == 2 perl ($value ) ? "-allnni":"" 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 $specify_runtype == 2 perl ($value ) ? "-djc":"" Avoid computing ML pairwise distances and BIONJ tree. use_fasttreesearch Turn on the fast tree search mode (-fast) perl $specify_runtype == 2 perl ($value ) ? "-fast":"" Avoid computing ML pairwise distances and BIONJ tree. constraint_file Specify a topological constraint tree file in NEWICK format (-g) perl $specify_runtype == 2 constraintfile.txt perl (defined $value ) ? "-g constraintfile.txt":"" Specify a topological constraint tree file in NEWICK format. The constraint tree can be a multifurcating tree and need not to include all taxa. num_parstrees Specify number of initial parsimony trees (-ninit) perl $specify_runtype == 2 perl (defined $value ) ? "-ninit $value":"" 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_runtype == 2 && $bootstrap_type ne "b" perl (defined $value ) ? "-n $value":"" 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_runtype == 2 perl (defined $value ) ? "-ntop $value":"" 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_runtype == 2 perl (defined $value ) ? "-nbest $value":"" 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_runtype == 2 perl (defined $value ) ? "-nstop $value":"" Specify number of unsuccessful iterations to stop. DEFAULT: 100 perturb_strength Perturbation strength (between 0 and 1) (-pers) perl $specify_runtype == 2 perl (defined $value ) ? "-pers $value":"" Specify perturbation strength (between 0 and 1) for randomized NNI. DEFAULT: 0.5 specify_radius SPR radius for the initial search (-sprrad) perl $specify_runtype == 2 perl (defined $value ) ? "-sprrad $value":"" Specify SPR radius for the initial parsimony tree search. DEFAULT: 6 ultrafast_search_params Bootstrap Search Parameters bootstrap_type Bootstrap Type bb b bo bc perl (defined $value ) ? "-$value $num_bootreps":"" bb 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) 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 perl (defined $part_resample) ? "-bspec $part_resample":"" part_resample2 perl $which_iqtree < 19 && $use_bnni perl (defined $part_resample) ? "-bspec $part_resample -keep_empty_seq":"" part_resample3 perl $which_iqtree > 200 && !$use_bnni perl (defined $part_resample ) ? "-bsam $part_resample":"" part_resample4 perl $which_iqtree > 200 && $use_bnni 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 single_branchtest Single Branch Tests sh_test SH-Like Test (-alrt) perl $bootstrap_type ne "b" && $bootstrap_type ne "bo" && $bootstrap_type ne "bc" perl ($value) ? "-alrt $num_replicates":"" parametrical_test Run the parametricaLRT test (-alrt 0) perl $bootstrap_type ne "b" && $bootstrap_type ne "bo" && $bootstrap_type ne "bc" perl ($value) ? "-alrt 0":"" abayes_test Approximate Bayes test (-abayes) perl $bootstrap_type ne "b" && $bootstrap_type ne "bo" && $bootstrap_type ne "bc" perl ($value) ? "-abayes":"" lbp_test Fast local bootstrap probability (-lbp) perl $bootstrap_type ne "b" && $bootstrap_type ne "bo" && $bootstrap_type ne "bc" perl ($value) ? "-lbp $num_replicates":"" 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 perl $value ? "-asr":"" specify_ancestralthresh Specify minimum threshold of posterior probability for best ancestral state (-asr-min) perl $which_iqtree > 19 perl $value ? "-asr-min $value":"" specify_ancestraltree Specify a user-defined tree to determine ancestral sequences (-te) perl $which_iqtree > 19 ancestralseqs.tre perl defined $value ? "-te ancestralseqs.tre":"" tree_topology Tree Topology Tests specify_treefile Specify a file containing a set of trees (-z) treefile1.tre perl (defined $value) ? "-z treefile1.tre":"" num_rell Specify the number of RELL replicates (-zb) perl (defined $value) ? "-zb $value":"" Sorry, the number of RELL replicates cannot be less than 1,000 perl defined $num_rell && $num_rell < 1000 -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 ($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 perl ($value) ? "-te fixed_usertree.tre":"" -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. consensus_tree Consensus Trees tree_file1 Specify a file containing a set of trees treefile1.tre perl (defined $value) ? "-t treefile1.tre":"" compute_consensustree Compute consensus tree of the trees passed via -t (-con) perl defined $tree_file1 perl ($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 $tree_file1 perl ($value) ? "-net":"" min_threshold Specify a minimum threshold between 0 and 1 (-minsup) perl defined $tree_file1 perl ($value) ? "-minsup":"" burnin_value Specify a burn-in (-bi) perl defined $tree_file1 perl (defined $value) ? "-bi ($value)":"" target_treefile Specify an input “target” tree file (-sup) targetfile.tre perl (defined $value) ? "-sup targetfile.tre":"" -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. 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 perl (defined $value) ? "-prec $value":"" nodetarget_treefile Specify name of a node in -sup target tree (-suptag) perl (defined $value) ? "-suptag $value":"" robinsons_fouldsdist Computing Robinson's Foulds distances tree_file2 Specify a second set of trees treefile2.tre perl (defined $value) ? "-rf treefile2.tre":"" compute_rfdistances_all Compute all-to-all RF distances between all trees passed via -t (-rf_all) perl defined $tree_file1 perl ($value) ? "-rf_all":"" compute_rfdistances_adj Compute RF distances between adjacent trees passed via -t (-rf_adj) perl defined $tree_file1 perl ($value) ? "-rf_adj":"" specify_rfdistancestree Select file of adjacent trees to pass via -t rfdistance.tre perl ($value) ? "-t rfdistance.tre":"" generate_randomtrees Generate Random Trees num_taxa Specify number of taxa for the tree (-r) choose_randomtype Specify a model for the random trees -r -ru -rcat -rbal -rcsg perl (defined $value) ? "$value $num_taxa":"" specify_brlengths Specify minimum, mean and maximum branch lengths of the random tree DEFAULT:-rlen 0.001 0.1 0.999 perl (defined $value) ? "-rlen $value":"" Specify three numbers: minimum, mean and maximum branch lengths of the random tree. cf_options Concordance Factor Options (Version 2 only) partition_modelfile Choose file that specifies the partition model (-p) perl ($value) ? "-p partition_file.txt":"" partition_file.txt partition_modelfile2 Choose file that specifies the model selection (-S) perl ($value) ? "-S partition_file.txt":"" partition_file.txt partition_tfile Choose a reference tree file for gcf (-t) perl (defined $value) ? "-t concat.treefile":"" concat.treefile setoftrees_file Choose a set of trees for gcf (-gcf) perl (defined $value) ? "-gcf loci.treefile":"" loci.treefile specify_numquartets Specify number of quartets (--scf) perl (defined $value) ? "--scf $value":"" The authors recommend at least 100 quartets for stable values perl (defined $specify_numquartets) && $specify_numquartets < 100 dating_options Dating Options (Version 2 only) specify_datefile Choose a file that specifies dates (--date) perl (defined $value) ? "--date date_file.txt":"" date_file.txt extract_datefile Automatically extract dates from taxon Names (--date TAXNAME) perl ($value) ? "--date TAXNAME":"" specify_datetip Specify tip dates as a real number or YYYY-MM-DD (--date-tip) perl (defined $value) ? "--date-tip $value":"" specify_rootdate Specify root date as a real number or YYYY-MM-DD (--date-root) perl (defined $value) ? "--date-root $value":"" specify_datetreefile Load and fix this tree topology (--te) perl (defined $value) ? "--date treetopology.txt":"" treetopology.txt specify_resampleint Resample branch lengths to infer the confidence interval (--date-ci) perl (defined $value) ? "--date-ci $value":"" specify_outlierthresh z-score threshold to detect outliers (--date-outlier) perl (defined $value) ? "--date-outlier $value":"" misc_options Miscellaneous Options print_sitestats Print alignment site statistics to.alninfofile (-alninfo) perl ($value) ? "-alninfo":"" fix_branchlengths Fix branch lengths of tree passed via -te. (-blfix) perl ($value) ? "-blfix fixbranchlengths.tre":"" branchlengths_tree Provide a tree to fix branch lengths(-te) fixbranchlengths.tre Please provide a tree for fixing branch lengths perl $fix_branchlengths && !defined $branchlengths_tree specify_minbranchlength Specify minimum branch length. (-blmin) perl ($value) ? "-blmin":"" specify_maxbranchlength Specify maximum branch length. (-blmax) 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 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 $specify_runtype == 2 perl ($value ) ? "-wsr":"" per_sitewslfile Write site log-liklihoods to .sitelh file (-wsl) perl $specify_runtype == 2 perl ($value ) ? "-wsl":"" per_sitewslrfile Write site log-likelihoods per rate category (-wslr) perl $specify_runtype == 2 perl ($value ) ? "-wslr":"" per_sitewslmfile Write site log-likelihoods per mixture class (-wslm) perl $specify_runtype == 2 perl ($value ) ? "-wslm":"" per_sitewslmrfile Write site log-likelihoods per mixture+rate class (-wslmr) perl $specify_runtype == 2 perl ($value ) ? "-wslmr":"" per_sitewspmfile Write site probabilities per mixture class (-wspm) perl $specify_runtype == 2 perl ($value ) ? "-wspm":"" per_sitewsprfile Write site probabilities per rate category (-wspr) perl $specify_runtype == 2 perl ($value ) ? "-wspr":"" per_sitewspmrfile Write site probabilities per rate category (-wspmr) perl $specify_runtype == 2 perl ($value ) ? "-wspmr":"" per_sitewplfile Write partition log-likelihoods to .partlh file (-wpl) perl $specify_runtype == 2 perl ($value ) ? "-wpl":"" write_sitelikelihoods Write log-likelihoods in TREE-PUZZLE format (-wsl) perl ($value) ? "-wsl":"" Turn on writing site log-likelihoods to .sitelh file in TREE-PUZZLE format. Such file can then be passed on to CONSEL for further tree tests. DEFAULT: OFF write_loglikelihoods Write log-likelihoods per rate category (-wslg) perl ($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 perl (defined $value) ? "-fconst integerfile.csv":"" 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. results *