iqtree(1)

GENERAL OPTIONS:

-? or -h

Print this help dialog

-version

Display version number

-s <alignment>

Input alignment in PHYLIP/FASTA/NEXUS/CLUSTAL/MSF format

-st <data_type>

BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect)

-q <partition_file>

Edge-linked partition model (file in NEXUS/RAxML format)

-spp <partition_file> Like -q option but allowing partition-specific rates

-sp <partition_file> Edge-unlinked partition model (like -M option of RAxML)

-t <start_tree_file> or -t BIONJ or -t RANDOM

Starting tree (default: 99 parsimony tree and BIONJ)

-te <user_tree_file> Like -t but fixing user tree (no tree search performed)

-o <outgroup_taxon>

Outgroup taxon name for writing .treefile

-pre <PREFIX>

Prefix for all output files (default: aln/partition)

-nt <num_threads>

Number of cores/threads or AUTO for automatic detection

-ntmax <max_threads> Max number of threads by -nt AUTO (default: #CPU cores)

-seed <number>

Random seed number, normally used for debugging purpose

-v, -vv, -vvv

Verbose mode, printing more messages to screen

-quiet

Quiet mode, suppress printing to screen (stdout)

-keep-ident

Keep identical sequences (default: remove & finally add)

-safe

Safe likelihood kernel to avoid numerical underflow

-mem RAM

Maximal RAM usage for memory saving mode

--runs NUMBER

Number of indepedent runs (default: 1)

CHECKPOINTING TO RESUME STOPPED RUN:

-redo

Redo analysis even for successful runs (default: resume)

-cptime <seconds>

Minimum checkpoint time interval (default: 60 sec)

LIKELIHOOD MAPPING ANALYSIS:

-lmap <#quartets>

Number of quartets for likelihood mapping analysis

-lmclust <clustfile> NEXUS file containing clusters for likelihood mapping

-wql

Print quartet log-likelihoods to .quartetlh file

NEW STOCHASTIC TREE SEARCH ALGORITHM:

-ninit <number>

Number of initial parsimony trees (default: 100)

-ntop <number>

Number of top initial trees (default: 20)

-nbest <number>

Number of best trees retained during search (defaut: 5)

-n <#iterations>

Fix number of iterations to stop (default: auto)

-nstop <number>

Number of unsuccessful iterations to stop (default: 100)

-pers <proportion>

Perturbation strength for randomized NNI (default: 0.5)

-sprrad <number>

Radius for parsimony SPR search (default: 6)

-allnni

Perform more thorough NNI search (default: off)

-g <constraint_tree> (Multifurcating) topological constraint tree file

-fast

Fast search to resemble FastTree

ULTRAFAST BOOTSTRAP:

-bb <#replicates>

Ultrafast bootstrap (>=1000)

-bsam GENE|GENESITE

Resample GENE or GENE+SITE for partition (default: SITE)

-wbt

Write bootstrap trees to .ufboot file (default: none)

-wbtl

Like -wbt but also writing branch lengths

-nm <#iterations>

Maximum number of iterations (default: 1000)

-nstep <#iterations> #Iterations for UFBoot stopping rule (default: 100)

-bcor <min_corr>

Minimum correlation coefficient (default: 0.99)

-beps <epsilon>

RELL epsilon to break tie (default: 0.5)

-bnni

Optimize UFBoot trees by NNI on bootstrap alignment

-j <jackknife>

Proportion of sites for jackknife (default: NONE)

STANDARD NON-PARAMETRIC BOOTSTRAP:

-b <#replicates>

Bootstrap + ML tree + consensus tree (>=100)

-bc <#replicates>

Bootstrap + consensus tree

-bo <#replicates>

Bootstrap only

SINGLE BRANCH TEST:

-alrt <#replicates>

SH-like approximate likelihood ratio test (SH-aLRT)

-alrt 0

Parametric aLRT test (Anisimova and Gascuel 2006)

-abayes

approximate Bayes test (Anisimova et al. 2011)

-lbp <#replicates>

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 TESTMERGEONLY

Find best partition scheme (like PartitionFinder)

-m TESTMERGE

Find best partition scheme followed by tree inference

-m MF+MERGE

Find best partition scheme incl. FreeRate heterogeneity

-m MFP+MERGE

Like -m MF+MERGE followed by tree inference

-rcluster <percent>

Percentage of partition pairs (relaxed clustering alg.)

-rclusterf <perc.>

Percentage of partition pairs (fast relaxed clustering)

-rcluster-max <num>

Max number of partition pairs (default: 10*#partitions)

-mset program

Restrict search to models supported by other programs (raxml, phyml or mrbayes)

-mset <lm-subset>

Restrict search to a subset of the Lie-Markov models Options for lm-subset are: liemarkov, liemarkovry, liemarkovws, liemarkovmk, strandsymmetric

-mset m1,...,mk

Restrict search to models in a comma-separated list (e.g. -mset WAG,LG,JTT)

-msub source

Restrict search to AA models for specific sources (nuclear, mitochondrial, chloroplast or viral)

-mfreq f1,...,fk

Restrict search to using a list of state frequencies (default AA: -mfreq FU,F; codon: -mfreq ,F1x4,F3x4,F)

-mrate r1,...,rk

Restrict search to a list of rate-across-sites models (e.g. -mrate E,I,G,I+G,R is used for -m MF)

-cmin <kmin>

Min #categories for FreeRate model [+R] (default: 2)

-cmax <kmax>

Max #categories for FreeRate model [+R] (default: 10)

-merit AIC|AICc|BIC

Optimality criterion to use (default: all)

-mtree

Perform full tree search for each model considered

-mredo

Ignore model results computed earlier (default: reuse)

-madd mx1,...,mxk

List of mixture models to also consider

-mdef <nexus_file>

A model definition NEXUS file (see Manual)

SUBSTITUTION MODEL:

-m <model_name>

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

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: One of the following, optionally prefixed by RY, WS or MK:

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

Non-reversible: STRSYM (strand symmetric model, synonymous with WS6.6) Non-reversible: UNREST (most general unrestricted model, functionally equivalent to 12.12) Models can have parameters appended in brackets.

e.g. '-mRY3.4{0.2,-0.3}+I' specifies parameters for RY3.4 model but leaves proportion of invariant sites unspecified. '-mRY3.4{0.2,-0.3}+I{0.5} gives both. When this is done, the given parameters will be taken as fixed (default) or as start point for optimization (if -optfromgiven option supplied)

Otherwise: Name of file containing user-model parameters

(rate parameters and state frequencies)

STATE FREQUENCY:

Append one of the following +F... to -m <model_name> +F Empirically counted frequencies from alignment +FO (letter-O) Optimized frequencies by maximum-likelihood +FQ Equal frequencies +FRY, +FWS, +FMK For DNA models only, +FRY is freq(A+G)=1/2=freq(C+T),

+FWS is freq(A+T)=1/2=freq(C+G), +FMK is freq(A+C)=1/2=freq(G+T).

+F####

where # are digits - for DNA models only, for basis in ACGT order, digits indicate which frequencies are constrained to be the same. E.g. +F1221 means freq(A)=freq(T), freq(C)=freq(G).

+FU

Amino-acid frequencies by the given protein matrix

+F1x4 (codon model)

Equal NT frequencies over three codon positions

+F3x4 (codon model)

Unequal NT frequencies over three codon positions

MIXTURE MODEL:

-m "MIX{model1,...,modelK}"

Mixture model with K components

-m "FMIX{freq1,...freqK}"

Frequency mixture model with K components

-mwopt

Turn on optimizing mixture weights (default: none)

RATE HETEROGENEITY AMONG SITES:

-m modelname+I

A proportion of invariable sites

-m modelname+G[n]

Discrete Gamma model with n categories (default n=4)

-m modelname*G[n]

Discrete Gamma model with unlinked model parameters

-m modelname+I+G[n]

Invariable sites plus Gamma model with n categories

-m modelname+R[n]

FreeRate model with n categories (default n=4)

-m modelname*R[n]

FreeRate model with unlinked model parameters

-m modelname+I+R[n]

Invariable sites plus FreeRate model with n categories

-m modelname+Hn

Heterotachy model with n classes

-m modelname*Hn

Heterotachy model with n classes and unlinked parameters

-a <Gamma_shape>

Gamma shape parameter for site rates (default: estimate)

-amin <min_shape>

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

-gmedian

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

--opt-gamma-inv

More thorough estimation for +I+G model parameters

-i <p_invar>

Proportion of invariable sites (default: estimate)

-wsr

Write site rates to .rate file

-mh

Computing site-specific rates to .mhrate file using Meyer & von Haeseler (2003) method

POLYMORPHISM AWARE MODELS (PoMo):

-s <counts_file>

Input counts file (see manual)

-m <MODEL>+P

DNA substitution model (see above) used with PoMo

+N<POPSIZE>

Virtual population size (default: 9)

+[WB|WH|S]

Sampling method (default: +WB), WB: Weighted binomial, WH: Weighted hypergeometric S: Sampled sampling

+G[n]

Discrete Gamma rate model with n categories (default n=4)

ASCERTAINMENT BIAS CORRECTION:

-m modelname+ASC

Correction for absence of invariant sites in alignment

SINGLE TOPOLOGY HETEROTACHY MODEL:

-m <model_name>+H[k]

Heterotachy model mixed branch lengths with k classes

-m "MIX{m1,...mK}+H"

-nni-eval <m>

Loop m times for NNI evaluation (default m=1)

SITE-SPECIFIC FREQUENCY MODEL:

-ft <tree_file>

Input tree to infer site frequency model

-fs <in_freq_file>

Input site frequency model file

-fmax

Posterior maximum instead of mean approximation

CONSENSUS RECONSTRUCTION:

-t <tree_file>

Set of input trees for consensus reconstruction

-minsup <threshold>

Min split support in range [0,1]; 0.5 for majority-rule consensus (default: 0, i.e. extended consensus)

-bi <burnin>

Discarding <burnin> trees at beginning of <treefile>

-con

Computing consensus tree to .contree file

-net

Computing consensus network to .nex file

-sup <target_tree>

Assigning support values for <target_tree> to .suptree

-suptag <name>

Node name (or ALL) to assign tree IDs where node occurs

ROBINSON-FOULDS DISTANCE:

-rf_all

Computing all-to-all RF distances of trees in <treefile>

-rf <treefile2>

Computing all RF distances between two sets of trees stored in <treefile> and <treefile2>

-rf_adj

Computing RF distances of adjacent trees in <treefile>

TREE TOPOLOGY TEST:

-z <trees_file>

Evaluating a set of user trees

-zb <#replicates>

Performing BP,KH,SH,ELW tests for trees passed via -z

-zw

Also performing weighted-KH and weighted-SH tests

-au

Also performing approximately unbiased (AU) test

ANCESTRAL STATE RECONSTRUCTION:

-asr

Ancestral state reconstruction by empirical Bayes

-asr-min <prob>

Min probability of ancestral state (default: equil freq)

GENERATING RANDOM TREES:

-r <num_taxa>

Create a random tree under Yule-Harding model

-ru <num_taxa>

Create a random tree under Uniform model

-rcat <num_taxa>

Create a random caterpillar tree

-rbal <num_taxa>

Create a random balanced tree

-rcsg <num_taxa>

Create a random circular split network

-rlen <min_len> <mean_len> <max_len>

min, mean, and max branch lengths of random trees

MISCELLANEOUS:

-wt

Write locally optimal trees into .treels file

-blfix

Fix branch lengths of user tree passed via -te

-blscale

Scale branch lengths of user tree passed via -t

-blmin

Min branch length for optimization (default 0.000001)

-blmax

Max branch length for optimization (default 100)

-wsr

Write site rates and categories to .rate file

-wsl

Write site log-likelihoods to .sitelh file

-wslr

Write site log-likelihoods per rate category

-wslm

Write site log-likelihoods per mixture class

-wslmr

Write site log-likelihoods per mixture+rate class

-wspr

Write site probabilities per rate category

-wspm

Write site probabilities per mixture class

-wspmr

Write site probabilities per mixture+rate class

-wpl

Write partition log-likelihoods to .partlh file

-fconst f1,...,fN

Add constant patterns into alignment (N=#nstates)

-me <epsilon>

LogL epsilon for parameter estimation (default 0.01)

--no-outfiles

Suppress printing output files

--eigenlib

Use Eigen3 library

-alninfo

Print alignment sites statistics to .alninfo

-czb

Collapse zero branches in final tree

--show-lh

Compute tree likelihood without optimisation