iqtree2(1)

iqtree21

Efficient phylogenetic software by maximum likelihood

Usage

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

Overview

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

Releases

2 releases since Debian 12 (Bookworm); the text changed 1 time.

12
13

$ iqtree2

Pick options to build a command. 156 options jk move x pick y copy / filter [] section