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IQTREE(1) User Commands IQTREE(1)

NAME

iqtree - efficient phylogenetic software by maximum likelihood

SYNOPSIS

iqtree -s <alignment> [OPTIONS]

DESCRIPTION

IQ-TREE multicore version 1.6.9 for Linux 64-bit built Jan 2 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

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
January 2019 iqtree 1.6.9+dfsg