IQTREE3-OMP(1)

📦 version 3.1.1, in ubuntu stonking

iqtree3-omp(1) — User Commands. Multiprocessor version, bestie! 💅

💖 NAME 💖

iqtree3-omp — efficient phylogenetic software by maximum likelihood (multiprocessor version). No cap, she's iconic. 👑

🦋 SYNOPSIS 🦋

iqtree [-s ALIGNMENT] [-p PARTITION] [-m MODEL] [-t TREE] ...

🌸 DESCRIPTION 🌸

IQ-TREE version 3.1.1 for Linux x86 64-bit built Jul 28 2026. Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren. Contributed by Lam-Tung Nguyen, Dominik Schrempf, Chris Bielow, Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt. ✨

✨ GENERAL OPTIONS ✨

-h, --help — Print (more) help usages 💖
-s FILE[,...,FILE] — PHYLIP/FASTA/NEXUS/CLUSTAL/MSF alignment file(s) 🧬
-s DIR — Directory of alignment files 📁
--seqtype STRING — BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect)
-t FILE|PARS|RAND — Starting tree (default: 99 parsimony and BIONJ) 🌳
-o TAX[,...,TAX] — Outgroup taxon (list) for writing .treefile
--prefix STRING — Prefix for all output files (default: aln/partition) 🏷️
--seed NUM — Random seed number, normally used for debugging purpose 🎲
--safe — Safe likelihood kernel to avoid numerical underflow 🛟
--mem NUM[G|M|%] — Maximal RAM usage in GB | MB | % 🧠
--runs NUM — Number of independent runs (default: 1) 🔁
-v, --verbose — Verbose mode, printing more messages to screen 🗣️
-V, --version — Display version number
--quiet — Quiet mode, suppress printing to screen (stdout) 🤫
-fconst f1,...,fN — Add constant patterns into alignment (N=no. states)
--epsilon NUM — Likelihood epsilon for parameter estimate (default 0.01)
-T NUM|AUTO — No. cores/threads or AUTO-detect (default: 1) ⚡
--threads-max NUM — Max number of threads for -T AUTO (default: all cores)

🎀 CHECKPOINT 🎀

--redo — Redo both ModelFinder and tree search 🔄
--redo-tree — Restore ModelFinder and only redo tree search
--undo — Revoke finished run, used when changing some options ↩️
--cptime NUM — Minimum checkpoint interval (default: 60 sec and adapt) ⏱️

💅 PARTITION MODEL 💅

-p FILE|DIR — NEXUS/RAxML partition file or directory with alignments. Edge-linked proportional partition model.
-q FILE|DIR — Like -p but edge-linked equal partition model
-Q FILE|DIR — Like -p but edge-unlinked partition model
-S FILE|DIR — Like -p but separate tree inference
--subsample NUM — Randomly sub-sample partitions (negative for complement) 🎲
--subsample-seed NUM — Random number seed for --subsample

🧬 LIKELIHOOD/QUARTET MAPPING 🧬

--lmap NUM — Number of quartets for likelihood mapping analysis
--lmclust FILE — NEXUS file containing clusters for likelihood mapping
--quartetlh — Print quartet log-likelihoods to .quartetlh file

🌳 TREE SEARCH ALGORITHM 🌳

--ninit NUM — Number of initial parsimony trees (default: 100)
--ntop NUM — Number of top initial trees (default: 20)
--nbest NUM — Number of best trees retained during search (default: 5)
-n NUM — Fix number of iterations to stop (default: OFF)
--nstop NUM — Number of unsuccessful iterations to stop (default: 100)
--perturb NUM — Perturbation strength for randomized NNI (default: 0.5)
--radius NUM — Radius for parsimony SPR search (default: 6)
--allnni — Perform more thorough NNI search (default: OFF)
-g FILE — (Multifurcating) topological constraint tree file
--fast — Fast search to resemble FastTree 🚀
--polytomy — Collapse near-zero branches into polytomy
--tree-fix — Fix -t tree (no tree search performed)
--treels — Write locally optimal trees into .treels file
--show-lh — Compute tree likelihood without optimisation
--terrace — Check if the tree lies on a phylogenetic terrace

⚡ ULTRAFAST BOOTSTRAP/JACKKNIFE ⚡

-B, --ufboot NUM — Replicates for ultrafast bootstrap (>=1000)
-J, --ufjack NUM — Replicates for ultrafast jackknife (>=1000)
--jack-prop NUM — Subsampling proportion for jackknife (default: 0.5)
--sampling STRING — GENE|GENESITE resampling for partitions (default: SITE)
--boot-trees — Write bootstrap trees to .ufboot file (default: none)
--wbtl — Like --boot-trees but also writing branch lengths
--nmax NUM — Maximum number of iterations (default: 1000)
--nstep NUM — Iterations for UFBoot stopping rule (default: 100)
--bcor NUM — Minimum correlation coefficient (default: 0.99)
--beps NUM — RELL epsilon to break tie (default: 0.5)
--bnni — Optimize UFBoot trees by NNI on bootstrap alignment

🎲 NON-PARAMETRIC BOOTSTRAP/JACKKNIFE 🎲

-b, --boot NUM — Replicates for bootstrap + ML tree + consensus tree
-j, --jack NUM — Replicates for jackknife + ML tree + consensus tree
--jack-prop NUM — Subsampling proportion for jackknife (default: 0.5)
--bcon NUM — Replicates for bootstrap + consensus tree
--bonly NUM — Replicates for bootstrap only
--tbe — Transfer bootstrap expectation

🔬 SINGLE BRANCH TEST 🔬

--alrt NUM — Replicates for SH approximate likelihood ratio test
--alrt 0 — Parametric aLRT test (Anisimova and Gascuel 2006)
--abayes — approximate Bayes test (Anisimova et al. 2011)
--lbp NUM — Replicates for fast local bootstrap probabilities

🤖 MODEL-FINDER 🤖

--use-nn-model — Use neural network for tree inference
--nn-path-model — Neural network file for substitution model (onnx format)
--nn-path-rates — Neural network file for alpha value (onnx format)
-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 ...+LM — Additionally test Lie Markov models
-m ...+LMRY — Additionally test Lie Markov models with RY symmetry
-m ...+LMWS — Additionally test Lie Markov models with WS symmetry
-m ...+LMMK — Additionally test Lie Markov models with MK symmetry
-m ...+LMSS — Additionally test strand-symmetric models
--mset STRING — Restrict search to models supported by other programs (raxml, phyml, mrbayes, beast1 or beast2) If mrbayes is selected, will output a MrBayes Block File if Data Type is supported.
--mset STR,... — Comma-separated model list (e.g. -mset WAG,LG,JTT)
--msub STRING — Amino-acid model source (nuclear, mitochondrial, chloroplast or viral)
--mfreq STR,... — List of state frequencies
--mrate STR,... — List of rate heterogeneity among sites (e.g. -mrate E,I,G,I+G,R is used for -m MF)
--cmin NUM — Min categories for FreeRate model [+R] (default: 2)
--cmax NUM — Max categories for FreeRate model [+R] (default: 10)
--merit AIC|AICc|BIC — Akaike|Bayesian information criterion (default: BIC)
--mtree — Perform full tree search for every model
--madd STR,... — List of mixture models to consider
--mdef FILE — Model definition NEXUS file (see Manual)
--modelomatic — Find best codon/protein/DNA models (Whelan et al. 2015)

🧩 PARTITION-FINDER 🧩

--merge — Merge partitions to increase model fit
--merge greedy|rcluster|rclusterf — Set merging algorithm (default: rclusterf)
--merge-model 1|all — Use only 1 or all models for merging (default: 1)
--merge-model STR,... — Comma-separated model list for merging
--merge-rate 1|all — Use only 1 or all rate heterogeneity (default: 1)
--merge-rate STR,... — Comma-separated rate list for merging
--rcluster NUM — Percentage of partition pairs for rcluster algorithm
--rclusterf NUM — Percentage of partition pairs for rclusterf algorithm
--rcluster-max NUM — Max number of partition pairs (default: 10*partitions)

🧬 SUBSTITUTION MODEL 🧬

-m STRING — Model name string (e.g. GTR+F+I+G)

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, FLAVI,
Q.LG, Q.pfam, Q.pfam_gb, Q.bird, Q.mammal, Q.insect, Q.plant, Q.yeast

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:

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 (optionally prefixed by RY, WS or MK)

Non-reversible:

STRSYM (strand symmetric model, equiv. WS6.6), NONREV, UNREST (unrestricted model, equiv. 12.12) NQ.pfam, NQ.bird, NQ.mammal, NQ.insect, NQ.plant, NQ.yeast

Otherwise:

Name of file containing user-model parameters

🌈 STATE FREQUENCY 🌈

-m ...+F — Empirically counted frequencies from alignment
-m ...+FO — Optimized frequencies by maximum-likelihood
-m ...+FQ — Equal frequencies
-m ...+FRY — For DNA, freq(A+G)=1/2=freq(C+T)
-m ...+FWS — For DNA, freq(A+T)=1/2=freq(C+G)
-m ...+FMK — For DNA, freq(A+C)=1/2=freq(G+T)
-m ...+Fabcd — 4-digit constraint on ACGT frequency (e.g. +F1221 means f_A=f_T, f_C=f_G)
-m ...+FU — Amino-acid frequencies given protein matrix
-m ...+F1x4 — Equal NT frequencies over three codon positions
-m ...+F3x4 — Unequal NT frequencies over three codon positions

🔥 RATE HETEROGENEITY AMONG SITES 🔥

-m ...+I — A proportion of invariable sites
-m ...+G[n] — Discrete Gamma model with n categories (default n=4)
-m ...*G[n] — Discrete Gamma model with unlinked model parameters
-m ...+I+G[n] — invariable sites PLUS the Gamma model, with n rate categories bestie 💅
-m ...+R[n] — FreeRate model, n categories (and yes, n=4 if you don't say) ✨
-m ...*R[n] — FreeRate but the model parameters are unlinked, they're doing their own thing fr
-m ...+I+R[n] — invariable sites plus FreeRate, n categories, the whole combo meal 🍓
-m ...+Hn — heterotachy model with n classes
-m ...*Hn — heterotachy with n classes and unlinked parameters
--alpha-min NUM — the minimum Gamma shape parameter for site rates (default: 0.02)
--gamma-median — use the median approximation for +G site rates (the default is mean, btw)
--rate — write the empirical Bayesian site rates out to a .rate file 📝
--mlrate — write maximum likelihood site rates out to a .mlrate file

🧬 POLYMORPHISM AWARE MODELS (PoMo) 🧬

-s FILE — the input counts file (peep the manual for this one)
-m ...+P — a DNA substitution model (any of the ones above) used together with PoMo
-m ...+N<POPSIZE> — set the virtual population size (default: 9)
-m ...+WB|WH|S] — weighted binomial sampling
-m ...+WH — weighted hypergeometric sampling
-m ...+S — sampled sampling
-m ...+G[n] — discrete Gamma rate with n categories (default n=4)

🎀 COMPLEX MODELS 🎀

-m "MIX{m1,...,mK}" — mixture model with K components
-m "FMIX{f1,...fK}" — frequency mixture model with K components
--mix-opt — optimize the mixture weights (default: detect)
-m ...+ASC — ascertainment bias correction
--tree-freq FILE — input tree used to infer the site frequency model
--site-freq FILE — input site frequency model file
--freq-max — posterior maximum instead of the mean approximation

🌸 TREE TOPOLOGY TEST 🌸

--trees FILE — a set of trees to evaluate log-likelihoods on
--test NUM — number of replicates for the topology test
--test-weight — perform weighted KH and SH tests
--test-au — the approximately unbiased (AU) test (Shimodaira 2002)
--au-epsilon NUM — epsilon for the AU test: if |deltaL| < NUM, the tree gets kept no matter what the p-value says (default: 0.001)
--sitelh — write site log-likelihoods into a .sitelh file

👑 ANCESTRAL STATE RECONSTRUCTION 👑

--ancestral — ancestral state reconstruction via empirical Bayes
--asr-min NUM — minimum probability for an ancestral state (default: equil freq)

💀 TEST OF SYMMETRY 💀

--symtest — perform three tests of symmetry
--symtest-only — run --symtest and then just exit
--symtest-remove-bad — run --symtest and remove the bad partitions
--symtest-remove-good — run --symtest and remove the good partitions
--symtest-type MAR|INT — use the MARginal or INTernal test when removing partitions
--symtest-pval NUMER — the p-value cutoff (default: 0.05)
--symtest-keep-zero — keep the NAs in the tests 🙈

🦋 CONCORDANCE FACTOR ANALYSIS 🦋

-t FILE — reference tree used to assign concordance factor
--gcf FILE — set of source trees for the gene concordance factor (gCF)
--df-tree — write the discordant trees associated with gDF1
--scf NUM — number of quartets for the site concordance factor (sCF)
--scfl NUM — same as --scf but it uses likelihood (this one's recommended, no cap)
-s FILE — sequence alignment for --scf
-p FILE|DIR — partition file or directory for --scf
--cf-verbose — write CF per tree/locus to cf.stat_tree/_loci
--cf-quartet — write sCF for all the resampled quartets into .cf.quartet

🌈 ALISIM: ALIGNMENT SIMULATOR 🌈

Usage:

iqtree --alisim <OUTPUT_PREFIX> [-m MODEL] [-t TREE] ...

--alisim OUTPUT_ALIGNMENT — switch AliSim ON and set the output alignment filename
-t TREE_FILE — set the input tree file name
--length LENGTH — set the length of the root sequence
--num-alignments NUMBER — set how many output datasets you want
--seqtype STRING — BIN, DNA, AA, CODON, MORPH{NUM_STATES} (default: auto-detect). For morphological data, 0<NUM_STATES<=32
--m MODEL_STRING — pick the evolutionary model. The Manual has more detail on this one
--mdef FILE — name of a NEXUS model file that defines new models (see the Manual)
--fundi TAXA_LIST,RHO — specify a list of taxa, and Rho (the Fundi weight) for the FunDi model
--indel <INS>,<DEL> — set the insertion and deletion rate of the indel model, relative to the substitution rate
--indel-size <INS_DIS>,<DEL_DIS> — set the insertion and deletion size distributions
--sub-level-mixture — turn on the feature that simulates a substitution-level mixture model
--no-unaligned — stop outputting a file of unaligned sequences when you're using indel models
--root-seq FILE,SEQ_NAME — specify the root sequence from an alignment
-s FILE — specify the input sequence alignment
--no-copy-gaps — stop copying gaps from the input alignment (default: false)
--site-freq <OPTION> — specify the option (MEAN (default), or SAMPLING, or MODEL) to mimic the site-frequencies for mixture models from the input alignment (see the Manual)
--site-rate <OPTION> — specify the option (MEAN (default), or SAMPLING, or MODEL) to mimic the discrete rate heterogeneity from the input alignment (see the Manual)
-t RANDOM{MODEL,NUM_TAXA} — specify the model and the number of taxa to generate a random tree
-rlen MIN MEAN MAX — give three numbers: minimum, mean and maximum branch lengths when generating a random tree
-p FILE — NEXUS/RAxML partition file, edge-linked proportional partition model
-q FILE — like -p but edge-linked equal partition model
-Q FILE — like -p but edge-unlinked partition model
--distribution FILE — hand over a definition file of distributions, which can be used to generate random model parameters
--branch-distribution DIS — specify a distribution that the branch lengths of the input trees get randomly generated from and overridden with
--branch-scale SCALE — specify a value to scale all branch lengths
--single-output — output all alignments into one single file
--write-all — turn on outputting internal sequences
--seed NUM — random seed number (default: CPU clock). Be careful — if you want your AliSim runs to be reproducible, you gotta specify the seed number, bestie
-gz — enable output compression, but it takes longer to run
-af phy|fasta — set the output format (default: phylip)

The User Manual is available at http://www.iqtree.org/doc/AliSim 🫶

💜 ANALYSIS WITH GENTRIUS ALGORITHM 💜

--gentrius FILE — the file has to contain either a single species-tree or a set of subtrees
-pr_ab_matrix FILE — presence-absence matrix of loci coverage
-s FILE — PHYLIP/FASTA/NEXUS/CLUSTAL/MSF alignment file(s)
-p FILE — NEXUS/RAxML partition file
-g_stop_t NUM — stop after NUM species-trees were generated, or use 0 to turn this stopping rule off. Default: 1MLN trees.
-g_stop_i NUM — stop after NUM intermediate trees were visited, or use 0 to turn this stopping rule off. Default: 10MLN trees.
-g_stop_h NUM — stop after NUM hours (CPU time), or use 0 to turn this stopping rule off. Default: 7 days.
-g_non_stop — turn off ALL the stopping rules 😳
-g_query FILE — species-trees to test for an identical set of subtrees
-g_print — write all generated species-trees. WARNING: there might be millions of trees!
-g_print_lim NUM — a limit on how many species-trees get written
-g_print_induced — write the induced partition subtrees
-g_print_m — write the presence-absence matrix
-g_rm_leaves NUM — invoke reverse analysis for the complex datasets

🦠 GENOMIC EPIDEMIOLOGICAL ANALYSIS 🦠

--pathogen — apply the CMAPLE tree search algorithm if the sequence divergence is low, otherwise apply the IQ-TREE algorithm
--pathogen-force — apply the CMAPLE tree search algorithm regardless of how divergent the sequences are
--alrt <num_rep> — specify the number of replicates to compute SH-aLRT
--sprta — compute SPRTA (DeMaio et al., 2024) branch supports
--sprta-zero-branch — compute SPRTA supports for zero-length branches
--sprta-other-places — output the alternative SPRs and their SPRTA supports
-T <num_thread> — specify the number of threads used to compute branch supports (SH-aLRT or SPRTA)

⭐ TIME TREE RECONSTRUCTION ⭐

--date FILE — file containing dates of tips or ancestral nodes
--date TAXNAME — pull the dates out of the taxon names, after the last '|'
--date-tip STRING — tip dates as a real number or YYYY-MM-DD
--date-root STRING — root date as a real number or YYYY-MM-DD
--date-ci NUM — number of replicates for computing the confidence interval
--clock-sd NUM — standard deviation for the lognormal relaxed clock (default: 0.2)
--date-no-outgroup — exclude the outgroup from the time tree
--date-outlier NUM — Z-score cutoff used to remove outlier tips/nodes (e.g. 3)
--date-options ".." — extra options that get passed straight through to LSD2
--dating STRING — dating method: LSD for least square dating (this is the default)

and that's a wrap on the iqtree3-omp page, bestie 🎀 this one ships as iqtree3-omp 3.1.1+dfsg, dated July 2026, and it lives at IQTREE3-OMP(1) — go read the manual and slay your phylogenies 💖✨

📦 where this page comes from

ubuntu stonking: iqtree3 3.1.1+dfsg-2build1 · GPL-2.0-or-later
💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on 2026-11-02: a language model's rewrite of the original, under its terms