IQTREE2-OMP(1)

📦

version 2.4.0 · 5 versions

🌸 IQTREE2-OMP(1) 🌸

okay so bestie, this is the manual page from the IQTREE2-OMP section of the manual, and it's all about a little program called iqtree2-omp. it's long, so we're doing it in parts — this is part 1, don't panic 💖

✨ NAME ✨

iqtree2-omp — efficient phylogenetic software by maximum likelihood (multiprocessor version) 🦋

✨ SYNOPSIS ✨

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

(yes the binary in the synopsis is literally iqtree, that's just how it is, iykyk 💅)

✨ DESCRIPTION ✨

IQ-TREE multicore version 2.4.0 for Linux x86 64-bit built Jul 28 2026 💻✨

Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong 👑 — absolute legends, no cap.

🌈 GENERAL OPTIONS:

-h, --help — prints (more) help usages. your friendly lil "what do i even do" button 🫶
-s FILE[,...,FILE] — PHYLIP/FASTA/NEXUS/CLUSTAL/MSF alignment file(s). feed it your data bestie 🌸
-s DIR — a whole directory of alignment files 📂
--seqtype STRING — the sequence type: BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect 🔍)
-t FILE|PARS|RAND — the starting tree (default: 99 parsimony and BIONJ 🌱)
-o TAX[,...,TAX] — outgroup taxon (or a whole list of them) for writing .treefile
--prefix STRING — prefix for all your output files (default: aln/partition) 🎀
--seed NUM — random seed number, normally used for debugging purpose 🎲
--safe — safe likelihood kernel to avoid numerical underflow (safety first diva 💅)
--mem NUM[G|M|%] — maximal RAM usage in GB | MB | %
--runs NUM — number of indepedent runs (default: 1)
-v, --verbose — verbose mode, prints more messages to screen 📢
-V, --version — display version number
--quiet — quiet mode, suppresses printing to screen (stdout) 🤫
-fconst f1,...,fN — add constant patterns into the 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 the 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 a 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 number = the 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 the .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 the -t tree (no tree search performed) 📌
--treels — write locally optimal trees into the .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 (must be >=1000) 🚀
-J, --ufjack NUM — replicates for ultrafast jackknife (must be >=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 the .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 the 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:

-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 the search to models supported by other programs (raxml, phyml, mrbayes, beast1 or beast2)
--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 the rcluster algorithm
--rclusterf NUM — percentage of partition pairs for the 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)

here's the big menu of model names, bestie, take your time 🍓

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,
Protein: 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 a file containing user-model parameters 📁

🌈 STATE FREQUENCY:

-m ...+F — empirically counted frequencies from the 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 Gamma model with n categories
-m ...+R[n] — FreeRate model with n categories (default n=4)
-m ...*R[n] — FreeRate model with unlinked model parameters
-m ...+I+R[n] — invariable sites plus FreeRate model with n categories
-m ...+Hn — heterotachy model with n classes
-m ...*Hn — the heterotachy model, bestie, with n classes and unlinked parameters — every class gets to keep its own settings, no sharing, no borrowing, main character energy only 💅
--alpha-min NUM — the minimum Gamma shape parameter for site rates (default: 0.02)
--gamma-median — use the median approximation for +G site rates (default is mean, jsyk 🙈)
--rate — write out empirical Bayesian site rates into a .rate file ✨
--mlrate — write out maximum likelihood site rates into a .mlrate file 🔥

🧬 POLYMORPHISM AWARE MODELS (PoMo) 🧬

-s FILE — the input counts file (go read the manual for this one, it's giving special)
-m ...+P — the DNA substitution model (the one from up above) that you use alongside PoMo
-m ...+N<POPSIZE> — 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 — use the posterior maximum instead of the mean approximation

🔍 TREE TOPOLOGY TEST 🔍

--trees FILE — a whole set of trees whose log-likelihoods get evaluated
--test NUM — how many replicates for the topology test
--test-weight — perform weighted KH and SH tests
--test-au — the approximately unbiased (AU) test (Shimodaira 2002)
--sitelh — write site log-likelihoods into a .sitelh file

👑 ANCESTRAL STATE RECONSTRUCTION 👑

--ancestral — ancestral state reconstruction, empirical Bayes style
--asr-min NUM — minimum probability of an ancestral state (default: equil freq)

🦋 TEST OF SYMMETRY 🦋

--symtest — run three tests of symmetry
--symtest-only — do --symtest then exist (yes, "exist", that's literally what it says and honestly, iconic)
--symtest-remove-bad — do --symtest and remove the bad partitions
--symtest-remove-good — do --symtest and remove the good partitions
--symtest-type MAR|INT — use the MARginal/INTernal test when you're 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 factors
--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 — like --scf but using likelihood (recommended 👀)
-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 resampled quartets to .cf.quartet

🧚 ALISIM: ALIGNMENT SIMULATOR 🧚

Usage, periodt:

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

--alisim OUTPUT_ALIGNMENT — activate AliSim and pick the output alignment filename
-t TREE_FILE — set the input tree file name
--length LENGTH — set how long the root sequence is
--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 — specify the evolutionary model. See the Manual for more detail
--mdef FILE — name of a NEXUS model file to define new models (see Manual)
--fundi TAXA_LIST,RHO — specify a list of taxa, and Rho (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 — enable the feature to simulate substitution-level mixture model
--no-unaligned — disable 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 — disable 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 Manual)
--site-rate <OPTION> — specify the option (MEAN (default), or SAMPLING, or MODEL) to mimic the discrete rate heterogeneity from the input alignment (see Manual)
-t RANDOM{MODEL,NUM_TAXA} — specify the model and the number of taxa to generate a random tree
-rlen MIN MEAN MAX — specify 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 — supply a definition file of distributions, which could be used to generate random model parameters
--branch-distribution DIS — specify a distribution, from which branch lengths of the input trees are randomly generated and overridden
--branch-scale SCALE — specify a value to scale all branch lengths
--single-output — output all alignments into a single file
--write-all — enable outputting internal sequences
--seed NUM — random seed number (default: CPU clock). Be careful ⚠️ — to make the AliSim reproducible, users should specify the seed number
-gz — enable output compression but taking longer running time
-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 must 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 off this stopping rule. Default: 1MLN trees
-g_stop_i NUM — stop after NUM intermediate trees were visited, or use 0 to turn off this stopping rule. Default: 10MLN trees
-g_stop_h NUM — stop after NUM hours (CPU time), or use 0 to turn off this stopping rule. Default: 7 days
-g_non_stop — turn off all 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 — limit on the number of species-trees to be written
-g_print_induced — write induced partition subtrees
-g_print_m — write presence-absence matrix
-g_rm_leaves NUM — invoke reverse analysis for complex datasets

💜 GENOMIC EPIDEMIOLOGICAL ANALYSIS 💜

--pathogen — apply the CMAPLE tree search algorithm if sequence divergence is low, otherwise, apply the IQ-TREE algorithm
--pathogen-force — apply the CMAPLE tree search algorithm regardless of sequence divergence

🎀 TIME TREE RECONSTRUCTION 🎀

--date FILE — file containing dates of tips or ancestral nodes
--date TAXNAME — extract dates from 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 to compute confidence interval
--clock-sd NUM — std-dev for lognormal relaxed clock (default: 0.2)
--date-no-outgroup — exclude outgroup from time tree
--date-outlier NUM — Z-score cutoff to remove outlier tips/nodes (e.g. 3)
--date-options ".." — extra options passing directly to LSD2
--dating STRING — dating method: LSD for least square dating (default)

And that's the whole thing, bestie 🫶 that was iqtree2-omp version 2.4.0+dfsg, dated July 2026, straight from the IQTREE2-OMP(1) page. Go forth and phylogeny ✨🌸

📦 where this page comes from

ubuntu stonking: iqtree 2.4.0+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