---
name: "iqtree2-omp"
section: "1"
platform: "linux"
package: "iqtree"
version: "2.0.7+dfsg-1+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/iqtree2-omp"
---

# iqtree2-omp(1)

efficient phylogenetic software by maximum likelihood (multiprocessor version)

## NAME

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

## SYNOPSIS

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

## DESCRIPTION

IQ-TREE multicore version 2.0.7 for Linux 64-bit built Nov 29 2024 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

### 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 indepedent 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 (defaut: 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:

- **-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 or mrbayes)

- **--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)

- 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

  Heterotachy model with n classes and unlinked parameters

- **--alpha-min** NUM

  Min Gamma shape parameter for site rates (default: 0.02)

- **--gamma-median**

  Median approximation for +G site rates (default: mean)

- **--rate**

  Write empirical Bayesian site rates to .rate file

- **--mlrate**

  Write maximum likelihood site rates to .mlrate file

### POLYMORPHISM AWARE MODELS (PoMo):

- **-s** FILE

  Input counts file (see manual)

- **-m** ...+P

  DNA substitution model (see above) used 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:

- **-m** "MIX{m1,...,mK}"

  Mixture model with K components

- **-m** "FMIX{f1,...fK}"

  Frequency mixture model with K components

- **--mix-opt**

  Optimize mixture weights (default: detect)

- **-m** ...+ASC

  Ascertainment bias correction

- **--tree-freq** FILE

  Input tree to infer site frequency model

- **--site-freq** FILE

  Input site frequency model file

- **--freq-max**

  Posterior maximum instead of mean approximation

### TREE TOPOLOGY TEST:

- **--trees** FILE

  Set of trees to evaluate log-likelihoods

- **--test** NUM

  Replicates for topology test

- **--test-weight**

  Perform weighted KH and SH tests

- **--test-au**

  Approximately unbiased (AU) test (Shimodaira 2002)

- **--sitelh**

  Write site log-likelihoods to .sitelh file

### ANCESTRAL STATE RECONSTRUCTION:

- **--ancestral**

  Ancestral state reconstruction by empirical Bayes

- **--asr-min** NUM

  Min probability of ancestral state (default: equil freq)

### TEST OF SYMMETRY:

- **--symtest**

  Perform three tests of symmetry

- **--symtest-only**

  Do **--symtest** then exist

- **--symtest-remove-bad**

  Do **--symtest** and remove bad partitions

- **--symtest-remove-good**

  Do **--symtest** and remove good partitions

- **--symtest-type** MAR\|INT

  Use MARginal/INTernal test when removing partitions

- **--symtest-pval** NUMER

  P-value cutoff (default: 0.05)

- **--symtest-keep-zero**

  Keep NAs in the tests

### CONCORDANCE FACTOR ANALYSIS:

- **-t** FILE

  Reference tree to assign concordance factor

- **--gcf** FILE

  Set of source trees for gene concordance factor (gCF)

- **--df-tree**

  Write discordant trees associated with gDF1

- **--scf** NUM

  Number of quartets for site concordance factor (sCF)

- **-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