IQTREE2-MPI(1)

📦
version 2.4.0 · 5 versions
, in ubuntu stonking

💖 IQTREE2-MPI — the manual page, but make it make sense 💖

okay bestie, this is iqtree2-mpi(1), aka the multiprocessor version of IQ-TREE2 — efficient phylogenetic software by maximum likelihood 🧬✨. It lives in the User Commands section of the manual, and it's lowkey a whole queen. Sit down, hydrate, and let's read her together 🫶

🌸 NAME 🌸

iqtree2-mpi — efficient phylogenetic software by maximum likelihood, but make it multiprocessor 💅 (that's the MPI version, iykyk).

✨ SYNOPSIS ✨

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

yes bestie, that's the whole vibe. Options go in, trees come out 🌳

👑 DESCRIPTION 👑

This is IQ-TREE MPI 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 icons, no cap 👑

🎀 GENERAL OPTIONS: 🎀

  • -h, --help — prints (even more) help usages, like she's not done explaining herself
  • -s FILE[,...,FILE] — your PHYLIP/FASTA/NEXUS/CLUSTAL/MSF alignment file(s) 💖
  • -s DIR — a whole directory of alignment files
  • --seqtype STRING — pick your type: BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect, she'll figure it out herself)
  • -t FILE|PARS|RAND — 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 output files (default: aln/partition)
  • --seed NUM — random seed number, normally used for debugging purposes 🔍
  • --safe — safe likelihood kernel, so you don't get numerical underflow (she's being careful 🥺)
  • --mem NUM[G|M|%] — maximal RAM usage in GB | MB | % 🧠
  • --runs NUM — number of independent runs (default: 1)
  • -v, --verbose — verbose mode, prints more messages to screen (she's a talker 💬)
  • -V, --version — display version number
  • --quiet — quiet mode, suppresses 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 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 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) — she's thorough 💅
  • -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 .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: 💅

  • -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)
  • --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 🌟

🎀 the -m flag herself

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

and now, bestie, the model menu. it's giving Cheesecake Factory menu. every single one is here 👇

🌸 DNA:

HKY (default), JC, F81, K2P, K3P, K81uf, TN/TrN, TNef, TIM, TIMef, TVM, TVMef, SYM, GTR, or a 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 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 parameters that are unlinked. Like, each class is living its own independent life 🦋
  • --alpha-min NUM — smallest Gamma shape parameter allowed for site rates (default: 0.02)
  • --gamma-median — use the median approximation for +G site rates (default is the mean, jsyk)
  • --rate — write the empirical Bayesian site rates out to a .rate file 📝
  • --mlrate — write the maximum likelihood site rates out to a .mlrate file ✨

🧬 POLYMORPHISM AWARE MODELS (PoMo) 💅

  • -s FILE — the input counts file (see the manual, iykyk)
  • -m ...+P — a DNA substitution model (the ones from up above) used together with 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 (she's complicated, and that's iconic) 👑

  • -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 is detect)
  • -m ...+ASC — ascertainment bias correction (no cap, this one is required a lot of the time)
  • --tree-freq FILE — an input tree, used to infer the site frequency model
  • --site-freq FILE — an input site frequency model file
  • --freq-max — use the posterior maximum instead of the mean approximation

🔥 TREE TOPOLOGY TEST 🔥

  • --trees FILE — the set of trees whose log-likelihoods you wanna evaluate
  • --test NUM — how many replicates for the topology test
  • --test-weight — do the weighted KH and SH tests
  • --test-au — the approximately unbiased (AU) test (Shimodaira 2002) 💫
  • --sitelh — write the site log-likelihoods out to a .sitelh file

🕯️ ANCESTRAL STATE RECONSTRUCTION 🕯️

  • --ancestral — ancestral state reconstruction via empirical Bayes
  • --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 (their spelling, not mine 😭 she's doing her best)
  • --symtest-remove-bad — do --symtest and yeet the bad partitions 🗑️
  • --symtest-remove-good — do --symtest and yeet the good partitions (yes, good, that's what it says 💀)
  • --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 — the reference tree used to assign the concordance factor
  • --gcf FILE — the set of source trees for the gene concordance factor (gCF)
  • --df-tree — write the discordant trees associated with gDF1
  • --scf NUM — the number of quartets for the site concordance factor (sCF)
  • --scfl NUM — like --scf but using likelihood (recommended, bestie, this is the one 🔥)
  • -s FILE — the sequence alignment for --scf
  • -p FILE|DIR — a 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 to .cf.quartet

🧚 ALISIM: ALIGNMENT SIMULATOR 🧚

Usage, verbatim, mwah:

iqtree --alisim <OUTPUT_PREFIX> [-m MODEL] [-t TREE] ...
  • --alisim OUTPUT_ALIGNMENT — activate AliSim and name 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 — specify the evolutionary model. See the Manual for more detail
  • --mdef FILE — the name of a NEXUS model file that defines new models (see Manual)
  • --fundi TAXA_LIST,RHO — a list of taxa plus 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 — enable simulating a substitution-level mixture model
  • --no-unaligned — disable outputting a file of unaligned sequences when 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 number of taxa to generate a random tree 🌳
  • -rlen MIN MEAN MAX — three numbers pls: 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 the 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 AliSim reproducible, users should specify the seed number ⚠️
  • -gz — enable output compression, but it takes 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 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 (chaos mode, go off queen 👑)
  • -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 the 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, no matter what 💪

⏳ 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 the confidence interval
  • --clock-sd NUM — std-dev for the lognormal relaxed clock (default: 0.2)
  • --date-no-outgroup — exclude the outgroup from the time tree
  • --date-outlier NUM — Z-score cutoff to remove outlier tips/nodes (e.g. 3)
  • --date-options ".." — extra options passed directly to LSD2
  • --dating STRING — dating method: LSD for least square dating (default)

and that's the whole page, bestie, you made it to the end 🎉 go run some phylogenies, you absolute genius 🫶

this was iqtree2-mpi version 2.4.0+dfsg, dated July 2026, and yes the man page itself is called IQTREE2-MPI(1) — love that for us 💖🌸✨

📦 where this page comes from