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This interface is used from the REST API to configure IQTREE runs.
The Tool ID for version 1 of this interface is toolid=IQTREE_XSEDE; the Tool ID for version 1.00.01 of this tool interface is tool=IQTREE_XSEDE_1_01_01
Version 1.01 adds the ability to provideup to five input data sets, each with a different datatype. The datatype must be specified correctly in the relevant partition file.
Specifically, the names of these files will be infile.txt, partition_datatype2.phy, partition_datatype3.phy, partition_datatype4.phy, partition_datatype5.phy.
The interface was updated 6/29/2021 to accomodate a change in the machine where these job run, and to fully support IQTree v. 2.x. A number of new features were introduced into the interface.
These are shown below in italics. Those shown in red may be critical.
Supported parameters:
all versions:
input.infile_ - Primary Input File (named infile.txt by the app.)
input.partition_file_ - Partition file
input.starting_tree_ - Specify a starting tree
input.constraint_file_ - Specify a topological constraint tree file in NEWICK format (-g)
input.specify_treefile_ - Specify a file containing a set of trees.
input.fixed_usertree_ - Specify a fixed user tree to estimate model parameters.
input.tree_file1_ - Specify a file containing a set of trees (For consensus trees.)
input.target_treefile_ - Specify an input “target” tree file (-sup); no default.
input.tree_file2_ - Specify a second tree file for Robinsons Foulds calculations.
input.specify_rfdistancestree_ - Select file of adjacent trees to pass via -t
input.specify_ancestraltree_ - Specify a user-defined tree to determine ancestral sequences (-te)
input.frequency_file_ - Specify a frequency file for PMSF analysis (-fs)
input.specify_nexusmodelfile_ - Specify a Nexus Model file. (-mdef)
input.datatype2_file_ - Select the file with your second datatype (partition_datatype5.phy)
input.datatype3_file_ - Select the file with your third datatype (partition_datatype5.phy)
input.datatype4_file_ - Select the file with your fourth datatype (partition_datatype5.phy)
input.datatype5_file_ - Select the file with your fifth datatype (partition_datatype5.phy)
vparam.runtime_ - (Float) - Maximum Hours to Run (up to 168 hours) default=0.5
vparam.which_iqtree_ - (Integer) - which version (16, 212) v.1.6.12 or v. 2.1.2; respectively. default=212
vparam.specify_numparts_ - (Integer) - How many partitions does your data set have. Deprecated
vparam.specify_numpatterns_ - (Integer) - Number of patterns in the data sets. Used to configure job. default=1000.
vparam.specify_mem_ - (Integer) - Memory required (in GB) (greater than 120 wont work, you get an error message). Deprecated
vparam.more_memory_ - (Switch) - I need more memory for a partitioned dataset run.
vparam.specify_safe_ - (Switch) - Safe likelihood kernel to avoid numerical underflow (-safe)
vparam.specify_autocores - (Switch) - Automatically select number of threads. IQTree V 1.6.12 only. This can only be specified when specify_runtype_=1. When specify_runtype=2, this option is automatic.
vparam.specify_runtype_ - (Excl) - Specify the nrun type; 1 (Model Selection); 2 (Tree Inference); no default. Required
vparam.sequence_type_ - (Excl) - Specify sequence type (-st); DNA; AA; BIN; MORPH; CODON; NT2AA (default = DNA). Not allowed with mixed_sequence option in v 1.01.
vparam.codon_type_ - (Excl) - Specify Codon type; CODON1; CODON2; CODON3; CODON4; CODON5; CODON6; CODON9; CODON10; CODON11; CODON12; CODON13<; CODON14; CODON16; CODON21; CODON22; CODON23; CODON24; CODON25 (Default=CODON1)
vparam.nt2aa_type_ - (Excl) - Specify translation table; NT2AA1; NT2AA2; NT2AA3; NT2AA4; NT2AA5; NT2AA6; NT2AA9; NT2AA10; NT2AA11; NT2AA12; NT2AA13; NT2AA14; NT2AA16; NT2AA21; NT2AA22; NT2AA23; NT2AA24; NT2AA25; (default=NT2AA1)
vparam.partition_type_ - (Excl) - Specify partition type; -q; -p; -Q; no default; required when partition_file is provided.
vparam.mixed_sequence_ - (Switch) - v 1.00.01+; I want to mix data types in a partitioned analysis
vparam.num_mixedsequences_ - (Excl) - v 1.00.01+ Number of data types in my partition file, (allowed 2, 3, 4, 5) no default
vparam.use_nj_ - (Switch) - Use a NJ starting tree (-t BIONJ); no default.
vparam.use_random_ - (Switch) - Use a Random starting tree (-t RANDOM); no default.
vparam.specify_outgroup_ - (String) - Specify an outgroup (-o); no default.
vparam.specify_prefix_ - (String) - Specify the prefix for output files (-pre); no default.
vparam.specify_seed_ - (Integer) - Specify a seed for the run (-seed); no default.
vparam.specify_quartets_ - (Integer) - Specify number of quartets (-lmap); no default.
Automatic Model Selection Parameters
vparam.specify_model_ - (Excl) - Test for the best model (-m TEST); TESTONLY; TEST; TESTNEWONLY; TESTNEW; TESTMERGEONLY; TESTMERGE; TESTNEWMERGEONLY; TESTNEWMERGEONLY; TESTNEWMERGE; no default.
vparam.specify_liemarkov_ (Excl) - Specify a Lie Markov Option +LM; +LMRY; +LMWS; +LMMK; +LMSS; +LM (no default)
vparam.select_rcluster_ (Excl) - Specify the relaxed clustering algorithm to use (-rcluster) -rcluster; -rclusterf; -rcluster-max (no default)
vparam.specify_rcluster_ - (Integer) - Specify the percentage for relaxed clustering algorithm (-rcluster); no default. deprecated.
vparam.specify_rclusterval - (Integer) - replaces specify_rcluster; Specify the percentage or max partition pairs for relaxed clustering algorithm.
vparam.specify_basemodels_ - (String) - 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; (no default).
vparam.specify_aamodels_ - (Excl) - Specify nuclear, mitochondrial, chloroplast or viral (-msub, protein); nuclear, mitochondrial, chloroplast, viral; no default.
vparam.specify_freqtypes_ - (String) - Specify a comma-separated list of frequency types for model selection (-mfreq) no default.
vparam.specify_ratehettypes_ - (String) Specify a comma-separated list of rate heterogeneity types for model selection (-mrate); no default.
vparam.specify_mincat_ - (Integer) - Specify minimum number of categories for FreeRate model (-cmin); no default.
vparam.specify_maxcat_ - (Integer) - Specify maximum number of categories for FreeRate model (-cmax); no default.
vparam.specify_merit_ - (String) - Specify either AIC, AICc or BIC for the optimality criterion (-merit); no default.
vparam.specify_fulltreesearch_ - (Switch) - Turn on full tree search for each model considered, to obtain more accurate result. (-mtree), no default.
vparam.specify_addlmodels_ - (String) - Specify a comma-separated list of mixture models to additionally consider for model selection. (-madd), no default.
Specify Substitution Models
vparam.freetextmodel_ - (String) - Specify any model as a free text string.
vparam.specify_dnamodel_ - (Excl) - Specify a DNA model (-m); JC69, F81, K80, HKY, TN93, TNe, K81, K81u, TPM2, TPM2u, TPM3, TPM3u, TIM, TIMe, TIM2, TIM2e, TIM3, TIM3e, TVM,TVMe, SYM, GTR; no default.
vparam.specify_protmodel_ - (Excl) - Specify a Protein model (-m); BLOSUM62, cpREV, Dayhoff, DCMut, FLU, HIVb, HIVw, JTT, JTTDCMut, LG, mtART, mtMAM, mtREV, mtZOA, Poisson, PMB, rtREV, VT, WAG, C10, C20, C30, C40, C50, C60, EX2, EX3, EHO, UL2, UL3, EX_EHO, LG4M, LG4X, CF4; mtMet; mtVer; mtInv. no default.
vparam.max_posteriormode_ - (Switch) - Switch to posterior maximum mode for obtaining site-specific profiles (-fmax)
vparam.specify_binmodel_ - (Excl) - Specify a Binary/Morphological model (-m ) JC2, GTR2, MK, ORDERED; no default.
vparam.specify_codonmodel_ - (Excl) - Specify a Codon model (-m ); MG; MGK, MG1KTS, MG1KTV, MG2K, GY, GY1KTS, GY1KTV, GY2K, KOSI07, ECMrest, SCHN05; no def ault.
vparam.specify_modelfreq_ - (Excl) - Specify model frequency; +F, +FO, +FQ,+F1x4, +F3x4; no default.
vparam.specify_modelrate_ - (Excl) - Specify rate heterogeneity; +I, +G, +I+G, +R, +I+R; no default.
vparam.asc_bias_ - (Excl) - Correct for Ascertainment bias (+ASC); +ASC; no default.
vparam.gamma_shape_ - (Float) - Specify the Gamma shape parameter (-a); no default.
vparam.median_approximation_ - (Switch) - Perform the median approximation for Gamma rate heterogeneity (-gmedian); no default.
vparam.invariable_sites_ - (Float) -Specify the proportion of invariable sites; no default.
vparam.thorough_estimation_ - (Switch) - Perform more thorough estimation for +I+G model parameters (--opt-gamma-inv); no default.
vparam.per_sitefile_ - (Switch) - Write per-site rates to .rate file (-wsr) no default.
Tree Search Parameters
vparam.num_parstrees_ - (Integer) - Specify number of initial parsimony trees (-ninit); no default.
vparam.num_topparstrees_ - (Integer) - Specify number of top initial parsimony trees (-ntop); no default.
vparam.num_besttrees_ - (Integer) - Number of trees in the candidate set to maintain (-nbest))
vparam.num_unsucctostop_ - (Integer) - Number of unsuccessful iterations to stop (-nstop); no default.
vparam.num_tostop_ - (Integer) - Number of iterations to stop (-n); no default.
vparam.specify_radius_ - (Integer) - SPR radius for the initial search (-sprrad); no default.
vparam.perturb_strength_ - (Float) - Perturbation strength (between 0 and 1) (-pers); no default.
vparam.slower_NNI_ - (Switch) - Turn on more thorough and slower NNI search (-allnni); no default.
vparam.no_mlpairwise_ - (Switch) - Avoid computing ML pairwise distances and BIONJ tree (-djc); no default.
vparam.use_fasttreesearch_ - (Switch) - Turn on the fast tree search mode (-fast)
Tree Search Parameters
vparam.bootstrap_type_ - (Excl) - Bootstrap Type; bb, b, bc; (default=bb)
vparam.num_bootreps_ - (Integer) - Specify number of bootstrap replicates (>=1000); no default.
vparam.write_boottrees_ - (Switch) - Turn on writing bootstrap trees to .ufboot file (-wbt); default=0.
vparam.write_boottrees1_ - (Switch) - Turn on writing bootstrap trees with branch lengths (-wbtl); default=0.
vparam.max_iters - (Integer) - Specify maximum number of iterations to stop. (-nm); default = 1000.
vparam.cc_ufboot_ - (Float) - Minimum correlation coefficient for UFBoot convergence criterion (-bcor); no default.
vparam.iter_interval_ - (Integer) - Iteration interval checking for UFBoot convergence (-nstep); no default.
vparam.specify_tiebreaker_ - (Float) - SPR radius for the initial search (-beps); no default.
vparam.part_resample_ - (Excl) - Resampling strategies for partitioned analysis (-bspec); GENE, GENESITE; no default.
Single Branch Tests
vparam.sh_test_ - (Switch) - SH-Like Test (-alrt); default=0.
vparam.abayes_test_ - (Switch) - Approximate Bayes test (-abayes); default=0.
vparam.lbp_test_ - (Switch) - Fast local bootstrap probability (-lbp); default=0.
vparam.num_replicates_ - (Integer) - Specify number of replicates (1000 or less); no default.
Tree Topology Tests
vparam.num_rell_ - (Integer) - Specify the number of RELL replicates (-zb)
vparam.weighted_tests_ - (Switch) - Perform the weighted-KH and weighted-SH tests; default=0.
vparam.unbiased_test_ - (Switch) - Perform the approximately unbiased (AU) test (-au); default=0.
vparam.estimate_parsetreeonly_ - (Switch) - Only estimate model parameters on an initial parsimony tree (-n 0)
Consensus Trees
vparam.compute_consensustree_ - (Switch) - Compute consensus tree of the trees passed via -t (-con). default=0.
vparam.compute_consensusnetwork_ - (Switch) - Compute consensus network of the trees passed via -t; default=0.
vparam.min_threshold_ - (Float) - Specify a minimum threshold between 0 and 1 (-minsup); no default.
vparam.burnin_value_ - (Integer) - Specify a burn-in (-bi); no default.
vparam.overwrite_logs_ - (Switch) - Overwrite existing log files (default=0).
vparam.nodetarget_treefile_ - (String) - Specify name of a node in -sup target tree (-suptag); no default.
vparam.set_precision_ - (String) - Set the precision of support values for -sup option (-prec)
vparam.set_scalefactor_ - (String) - Set the scaling factor of support values for -sup option (-scale)
Ancestral State Reconstruction
vparam.specify_ancestralthresh_ - (Float) - Specify minimum threshold of posterior probability for best ancestral state (-asr-min)
vparam.write_ancestralseqs_ - (Switch) - Write ancestral sequences to .statefile (-asr)
Computing Robinson's Foulds distances
vparam.compute_rfdistances_all_ - (Switch) - Compute all-to-all RF distances between all trees passed via -t (-rf_all); no default.
vparam.compute_rfdistances_adj_ - (Switch) - Compute RF distances between adjacent trees passed via -t (-rf_adj); no default.
