--- name: "iqtree-mpi" section: "1" platform: "linux" package: "iqtree" version: "1.6.12+dfsg-1" release: "Debian 11 (Bullseye)" platforms: ["linux"] url: "https://new.carta.tech/iqtree-mpi" --- # iqtree-mpi(1) efficient phylogenetic software by maximum likelihood (multiprocessor version) ## NAME iqtree-mpi - efficient phylogenetic software by maximum likelihood (multiprocessor version) ## SYNOPSIS **iqtree-mpi** *-s \* \[*OPTIONS*\] ## DESCRIPTION IQ-TREE MPI multicore version 1.6.12 for Linux 64-bit built Dec 4 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. ### GENERAL OPTIONS: - \-? or **-h** Print this help dialog - **-version** Display version number - **-s** \ Input alignment in PHYLIP/FASTA/NEXUS/CLUSTAL/MSF format - **-st** \ BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect) - **-q** \ Edge-linked partition model (file in NEXUS/RAxML format) **-spp** \ Like **-q** option but allowing partition-specific rates **-sp** \ Edge-unlinked partition model (like **-M** option of RAxML) - **-t** \ or **-t** BIONJ or **-t** RANDOM Starting tree (default: 99 parsimony tree and BIONJ) **-te** \ Like **-t** but fixing user tree (no tree search performed) - **-o** \ Outgroup taxon name for writing .treefile - **-pre** \ Prefix for all output files (default: aln/partition) - **-nt** \ Number of cores/threads or AUTO for automatic detection **-ntmax** \ Max number of threads by **-nt** AUTO (default: #CPU cores) - **-seed** \ Random seed number, normally used for debugging purpose - **-v**, **-vv**, **-vvv** Verbose mode, printing more messages to screen - **-quiet** Quiet mode, suppress printing to screen (stdout) - **-keep-ident** Keep identical sequences (default: remove & finally add) - **-safe** Safe likelihood kernel to avoid numerical underflow - **-mem** RAM Maximal RAM usage for memory saving mode - **--runs** NUMBER Number of indepedent runs (default: 1) ### CHECKPOINTING TO RESUME STOPPED RUN: - **-redo** Redo analysis even for successful runs (default: resume) - **-cptime** \ Minimum checkpoint time interval (default: 60 sec) ### LIKELIHOOD MAPPING ANALYSIS: - **-lmap** \<#quartets\> Number of quartets for likelihood mapping analysis **-lmclust** \ NEXUS file containing clusters for likelihood mapping - **-wql** Print quartet log-likelihoods to .quartetlh file ### NEW STOCHASTIC TREE SEARCH ALGORITHM: - **-ninit** \ Number of initial parsimony trees (default: 100) - **-ntop** \ Number of top initial trees (default: 20) - **-nbest** \ Number of best trees retained during search (defaut: 5) - **-n** \<#iterations\> Fix number of iterations to stop (default: auto) - **-nstop** \ Number of unsuccessful iterations to stop (default: 100) - **-pers** \ Perturbation strength for randomized NNI (default: 0.5) - **-sprrad** \ Radius for parsimony SPR search (default: 6) - **-allnni** Perform more thorough NNI search (default: off) **-g** \ (Multifurcating) topological constraint tree file - **-fast** Fast search to resemble FastTree ### ULTRAFAST BOOTSTRAP: - **-bb** \<#replicates\> Ultrafast bootstrap (\>=1000) - **-bsam** GENE\|GENESITE Resample GENE or GENE+SITE for partition (default: SITE) - **-wbt** Write bootstrap trees to .ufboot file (default: none) - **-wbtl** Like **-wbt** but also writing branch lengths - **-nm** \<#iterations\> Maximum number of iterations (default: 1000) **-nstep** \<#iterations\> #Iterations for UFBoot stopping rule (default: 100) - **-bcor** \ Minimum correlation coefficient (default: 0.99) - **-beps** \ RELL epsilon to break tie (default: 0.5) - **-bnni** Optimize UFBoot trees by NNI on bootstrap alignment - **-j** \ Proportion of sites for jackknife (default: NONE) ### STANDARD NON-PARAMETRIC BOOTSTRAP: - **-b** \<#replicates\> Bootstrap + ML tree + consensus tree (\>=100) - **-bc** \<#replicates\> Bootstrap + consensus tree - **-bo** \<#replicates\> Bootstrap only ### SINGLE BRANCH TEST: - **-alrt** \<#replicates\> SH-like approximate likelihood ratio test (SH-aLRT) - **-alrt** 0 Parametric aLRT test (Anisimova and Gascuel 2006) - **-abayes** approximate Bayes test (Anisimova et al. 2011) - **-lbp** \<#replicates\> Fast local bootstrap probabilities ### MODEL-FINDER: - **-m** TESTONLY Standard model selection (like jModelTest, ProtTest) - **-m** TEST Standard model selection followed by tree inference - **-m** MF Extended model selection with FreeRate heterogeneity - **-m** MFP Extended model selection followed by tree inference - **-m** TESTMERGEONLY Find best partition scheme (like PartitionFinder) - **-m** TESTMERGE Find best partition scheme followed by tree inference - **-m** MF+MERGE Find best partition scheme incl. FreeRate heterogeneity - **-m** MFP+MERGE Like **-m** MF+MERGE followed by tree inference - **-rcluster** \ Percentage of partition pairs (relaxed clustering alg.) - **-rclusterf** \ Percentage of partition pairs (fast relaxed clustering) - **-rcluster-max** \ Max number of partition pairs (default: 10\*#partitions) - **-mset** program Restrict search to models supported by other programs (raxml, phyml or mrbayes) - **-mset** \ Restrict search to a subset of the Lie-Markov models Options for lm-subset are: liemarkov, liemarkovry, liemarkovws, liemarkovmk, strandsymmetric - **-mset** m1,...,mk Restrict search to models in a comma-separated list (e.g. **-mset** WAG,LG,JTT) - **-msub** source Restrict search to AA models for specific sources (nuclear, mitochondrial, chloroplast or viral) - **-mfreq** f1,...,fk Restrict search to using a list of state frequencies (default AA: **-mfreq** FU,F; codon: **-mfreq** ,F1x4,F3x4,F) - **-mrate** r1,...,rk Restrict search to a list of rate-across-sites models (e.g. **-mrate** E,I,G,I+G,R is used for **-m** MF) - **-cmin** \ Min #categories for FreeRate model \[+R\] (default: 2) - **-cmax** \ Max #categories for FreeRate model \[+R\] (default: 10) - **-merit** AIC\|AICc\|BIC Optimality criterion to use (default: all) - **-mtree** Perform full tree search for each model considered - **-mredo** Ignore model results computed earlier (default: reuse) - **-madd** mx1,...,mxk List of mixture models to also consider - **-mdef** \ A model definition NEXUS file (see Manual) ### SUBSTITUTION MODEL: **-m** \ - DNA: HKY (default), JC, F81, K2P, K3P, K81uf, TN/TrN, TNef, TIM, TIMef, TVM, TVMef, SYM, GTR, or 6-digit model specification (e.g., 010010 = HKY) - Protein: LG (default), Poisson, cpREV, mtREV, Dayhoff, mtMAM, JTT, WAG, mtART, mtZOA, VT, rtREV, DCMut, PMB, HIVb, HIVw, JTTDCMut, FLU, Blosum62, GTR20, mtMet, mtVer, mtInv - Protein mixture: C10,...,C60, EX2, EX3, EHO, UL2, UL3, EX\_EHO, LG4M, LG4X - Binary: JC2 (default), GTR2 - Empirical codon: KOSI07, SCHN05 - Mechanistic codon: GY (default), MG, MGK, GY0K, GY1KTS, GY1KTV, GY2K, MG1KTS, MG1KTV, MG2K - Semi-empirical codon: XX\_YY where XX is empirical and YY is mechanistic model - Morphology/SNP: MK (default), ORDERED, GTR Lie Markov DNA: One of the following, optionally prefixed by RY, WS or MK: - 1\.1, 2\.2b, 3.3a, 3.3b, 3.3c, - 3\.4, 4\.4a, 4.4b, 4.5a, 4.5b, - 5\.6a, 5.6b, 5.7a, 5.7b, 5\.7c, - 5\.11a,5.11b,5.11c,5.16, 6\.6, - 6\.7a, 6.7b, 6.8a, 6.8b, 6\.17a, - 6\.17b,8.8, 8\.10a,8.10b, 8.16, - 8\.17, 8.18, 9.20a,9.20b,10.12, 10\.34,12.12 - Non-reversible: STRSYM (strand symmetric model, synonymous with WS6.6) Non-reversible: UNREST (most general unrestricted model, functionally equivalent to 12.12) Models can have parameters appended in brackets. - e.g. '-mRY3.4{0.2,-0.3}+I' specifies parameters for RY3.4 model but leaves proportion of invariant sites unspecified. '-mRY3.4{0.2,-0.3}+I{0.5} gives both. When this is done, the given parameters will be taken as fixed (default) or as start point for optimization (if **-optfromgiven** option supplied) - Otherwise: Name of file containing user-model parameters - (rate parameters and state frequencies) ### STATE FREQUENCY: - Append one of the following +F... to **-m** \ +F Empirically counted frequencies from alignment +FO (letter-O) Optimized frequencies by maximum-likelihood +FQ Equal frequencies +FRY, +FWS, +FMK For DNA models only, +FRY is freq(A+G)=1/2=freq(C+T), - \+FWS is freq(A+T)=1/2=freq(C+G), +FMK is freq(A+C)=1/2=freq(G+T). - \+F#### where # are digits - for DNA models only, for basis in ACGT order, digits indicate which frequencies are constrained to be the same. E.g. +F1221 means freq(A)=freq(T), freq(C)=freq(G). - \+FU Amino-acid frequencies by the given protein matrix - \+F1x4 (codon model) Equal NT frequencies over three codon positions - \+F3x4 (codon model) Unequal NT frequencies over three codon positions ### MIXTURE MODEL: - **-m** "MIX{model1,...,modelK}" Mixture model with K components - **-m** "FMIX{freq1,...freqK}" Frequency mixture model with K components - **-mwopt** Turn on optimizing mixture weights (default: none) ### RATE HETEROGENEITY AMONG SITES: - **-m** modelname+I A proportion of invariable sites - **-m** modelname+G\[n\] Discrete Gamma model with n categories (default n=4) - **-m** modelname\*G\[n\] Discrete Gamma model with unlinked model parameters - **-m** modelname+I+G\[n\] Invariable sites plus Gamma model with n categories - **-m** modelname+R\[n\] FreeRate model with n categories (default n=4) - **-m** modelname\*R\[n\] FreeRate model with unlinked model parameters - **-m** modelname+I+R\[n\] Invariable sites plus FreeRate model with n categories - **-m** modelname+Hn Heterotachy model with n classes - **-m** modelname\*Hn Heterotachy model with n classes and unlinked parameters - **-a** \ Gamma shape parameter for site rates (default: estimate) - **-amin** \ Min Gamma shape parameter for site rates (default: 0.02) - **-gmedian** Median approximation for +G site rates (default: mean) - **--opt-gamma-inv** More thorough estimation for +I+G model parameters - **-i** \ Proportion of invariable sites (default: estimate) - **-wsr** Write site rates to .rate file - **-mh** Computing site-specific rates to .mhrate file using Meyer & von Haeseler (2003) method ### POLYMORPHISM AWARE MODELS (PoMo): - **-s** \ Input counts file (see manual) - **-m** \+P DNA substitution model (see above) used with PoMo - \+N\ Virtual population size (default: 9) - \+\[WB\|WH\|S\] Sampling method (default: +WB), WB: Weighted binomial, WH: Weighted hypergeometric S: Sampled sampling - \+G\[n\] Discrete Gamma rate model with n categories (default n=4) ### ASCERTAINMENT BIAS CORRECTION: - **-m** modelname+ASC Correction for absence of invariant sites in alignment ### SINGLE TOPOLOGY HETEROTACHY MODEL: - **-m** \+H\[k\] Heterotachy model mixed branch lengths with k classes **-m** "MIX{m1,...mK}+H" - **-nni-eval** \ Loop m times for NNI evaluation (default m=1) ### SITE-SPECIFIC FREQUENCY MODEL: - **-ft** \ Input tree to infer site frequency model - **-fs** \ Input site frequency model file - **-fmax** Posterior maximum instead of mean approximation ### CONSENSUS RECONSTRUCTION: - **-t** \ Set of input trees for consensus reconstruction - **-minsup** \ Min split support in range \[0,1\]; 0.5 for majority-rule consensus (default: 0, i.e. extended consensus) - **-bi** \ Discarding \ trees at beginning of \ - **-con** Computing consensus tree to .contree file - **-net** Computing consensus network to .nex file - **-sup** \ Assigning support values for \ to .suptree - **-suptag** \ Node name (or ALL) to assign tree IDs where node occurs ### ROBINSON-FOULDS DISTANCE: - **-rf\_all** Computing all-to-all RF distances of trees in \ - **-rf** \ Computing all RF distances between two sets of trees stored in \ and \ - **-rf\_adj** Computing RF distances of adjacent trees in \ ### TREE TOPOLOGY TEST: - **-z** \ Evaluating a set of user trees - **-zb** \<#replicates\> Performing BP,KH,SH,ELW tests for trees passed via **-z** - **-zw** Also performing weighted-KH and weighted-SH tests - **-au** Also performing approximately unbiased (AU) test ### ANCESTRAL STATE RECONSTRUCTION: - **-asr** Ancestral state reconstruction by empirical Bayes - **-asr-min** \ Min probability of ancestral state (default: equil freq) ### GENERATING RANDOM TREES: - **-r** \ Create a random tree under Yule-Harding model - **-ru** \ Create a random tree under Uniform model - **-rcat** \ Create a random caterpillar tree - **-rbal** \ Create a random balanced tree - **-rcsg** \ Create a random circular split network - **-rlen** \ \ \ min, mean, and max branch lengths of random trees ### MISCELLANEOUS: - **-wt** Write locally optimal trees into .treels file - **-blfix** Fix branch lengths of user tree passed via **-te** - **-blscale** Scale branch lengths of user tree passed via **-t** - **-blmin** Min branch length for optimization (default 0.000001) - **-blmax** Max branch length for optimization (default 100) - **-wsr** Write site rates and categories to .rate file - **-wsl** Write site log-likelihoods to .sitelh file - **-wslr** Write site log-likelihoods per rate category - **-wslm** Write site log-likelihoods per mixture class - **-wslmr** Write site log-likelihoods per mixture+rate class - **-wspr** Write site probabilities per rate category - **-wspm** Write site probabilities per mixture class - **-wspmr** Write site probabilities per mixture+rate class - **-wpl** Write partition log-likelihoods to .partlh file - **-fconst** f1,...,fN Add constant patterns into alignment (N=#nstates) - **-me** \ LogL epsilon for parameter estimation (default 0.01) - **--no-outfiles** Suppress printing output files - **--eigenlib** Use Eigen3 library - **-alninfo** Print alignment sites statistics to .alninfo - **-czb** Collapse zero branches in final tree - **--show-lh** Compute tree likelihood without optimisation