.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH IQTREE "1" "February 2017" "iqtree 1.5.3+dfsg" "User Commands"
.SH NAME
iqtree \- efficient phylogenetic software by maximum likelihood
.SH SYNOPSIS
.B iqtree
\fI\,-s <alignment> \/\fR[\fI\,OPTIONS\/\fR]
.SH DESCRIPTION
IQ\-TREE version 1.5.3 for Linux 64\-bit built Feb 22 2017
Copyright \(co 2011\-2016 Nguyen Lam Tung, Olga Chernomor, Arndt von Haeseler and Bui Quang Minh.
.SS "GENERAL OPTIONS:"
.TP
\-? or \fB\-h\fR
Printing this help dialog
.TP
\fB\-s\fR <alignment>
Input alignment in PHYLIP/FASTA/NEXUS/CLUSTAL/MSF format
.TP
\fB\-st\fR <data_type>
BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto\-detect)
.TP
\fB\-q\fR <partition_file>
Edge\-linked partition model (file in NEXUS/RAxML format)
.HP
\fB\-spp\fR <partition_file> Like \fB\-q\fR option but allowing partition\-specific rates
.HP
\fB\-sp\fR <partition_file> Edge\-unlinked partition model (like \fB\-M\fR option of RAxML)
.TP
\fB\-t\fR <start_tree_file> or \fB\-t\fR BIONJ or \fB\-t\fR RANDOM
Starting tree (default: 99 parsimony tree and BIONJ)
.HP
\fB\-te\fR <user_tree_file> Like \fB\-t\fR but fixing user tree (no tree search performed)
.TP
\fB\-o\fR <outgroup_taxon>
Outgroup taxon name for writing .treefile
.TP
\fB\-pre\fR <PREFIX>
Using <PREFIX> for output files (default: aln/partition)
.TP
\fB\-seed\fR <number>
Random seed number, normally used for debugging purpose
.TP
\fB\-v\fR, \fB\-vv\fR, \fB\-vvv\fR
Verbose mode, printing more messages to screen
.TP
\fB\-quiet\fR
Silent mode, suppress printing to screen (stdout)
.TP
\fB\-keep\-ident\fR
Keep identical sequences (default: remove & finally add)
.TP
\fB\-safe\fR
Safe likelihood kernel to avoid numerical underflow
.TP
\fB\-mem\fR RAM
Maximal RAM usage for memory saving mode
.SS "CHECKPOINTING TO RESUME STOPPED RUN:"
.TP
\fB\-redo\fR
Redo analysis even for successful runs (default: resume)
.TP
\fB\-cptime\fR <seconds>
Minimum checkpoint time interval (default: 20)
.SS "LIKELIHOOD MAPPING ANALYSIS:"
.TP
\fB\-lmap\fR <#quartets>
Number of quartets for likelihood mapping analysis
.HP
\fB\-lmclust\fR <clustfile> NEXUS file containing clusters for likelihood mapping
.TP
\fB\-wql\fR
Print quartet log\-likelihoods to .quartetlh file
.SS "NEW STOCHASTIC TREE SEARCH ALGORITHM:"
.TP
\fB\-ninit\fR <number>
Number of initial parsimony trees (default: 100)
.TP
\fB\-ntop\fR <number>
Number of top initial trees (default: 20)
.TP
\fB\-nbest\fR <number>
Number of best trees retained during search (defaut: 5)
.TP
\fB\-n\fR <#iterations>
Fix number of iterations to <#iterations> (default: auto)
.TP
\fB\-nstop\fR <number>
Number of unsuccessful iterations to stop (default: 100)
.TP
\fB\-pers\fR <proportion>
Perturbation strength for randomized NNI (default: 0.5)
.TP
\fB\-sprrad\fR <number>
Radius for parsimony SPR search (default: 6)
.TP
\fB\-allnni\fR
Perform more thorough NNI search (default: off)
.HP
\fB\-g\fR <constraint_tree> (Multifurcating) topological constraint tree file
.SS "ULTRAFAST BOOTSTRAP:"
.TP
\fB\-bb\fR <#replicates>
Ultrafast bootstrap (>=1000)
.TP
\fB\-wbt\fR
Write bootstrap trees to .ufboot file (default: none)
.TP
\fB\-wbtl\fR
Like \fB\-wbt\fR but also writing branch lengths
.TP
\fB\-nm\fR <#iterations>
Maximum number of iterations (default: 1000)
.HP
\fB\-nstep\fR <#iterations> #Iterations for UFBoot stopping rule (default: 100)
.TP
\fB\-bcor\fR <min_corr>
Minimum correlation coefficient (default: 0.99)
.TP
\fB\-beps\fR <epsilon>
RELL epsilon to break tie (default: 0.5)
.SS "STANDARD NON-PARAMETRIC BOOTSTRAP:"
.TP
\fB\-b\fR <#replicates>
Bootstrap + ML tree + consensus tree (>=100)
.TP
\fB\-bc\fR <#replicates>
Bootstrap + consensus tree
.TP
\fB\-bo\fR <#replicates>
Bootstrap only
.SS "SINGLE BRANCH TEST:"
.TP
\fB\-alrt\fR <#replicates>
SH\-like approximate likelihood ratio test (SH\-aLRT)
.TP
\fB\-alrt\fR 0
Parametric aLRT test (Anisimova and Gascuel 2006)
.TP
\fB\-abayes\fR
approximate Bayes test (Anisimova et al. 2011)
.TP
\fB\-lbp\fR <#replicates>
Fast local bootstrap probabilities
.SS "AUTOMATIC MODEL SELECTION:"
.TP
\fB\-m\fR TESTONLY
Standard model selection (like jModelTest, ProtTest)
.TP
\fB\-m\fR TEST
Like \fB\-m\fR TESTONLY but followed by tree reconstruction
.TP
\fB\-m\fR TESTNEWONLY
Extended model selection incl. FreeRate (+R) heterogeneity
.TP
\fB\-m\fR TESTNEW
Like \fB\-m\fR TESTNEWONLY but followed by tree reconstruction
.TP
\fB\-m\fR TESTMERGEONLY
Select best\-fit partition scheme (like PartitionFinder)
.TP
\fB\-m\fR TESTMERGE
Like \fB\-m\fR TESTMERGEONLY but followed by tree reconstruction
.TP
\fB\-m\fR TESTNEWMERGEONLY
Like \fB\-m\fR TESTMERGEONLY but includes FreeRate heterogeneity
.TP
\fB\-m\fR TESTNEWMERGE
Like \fB\-m\fR TESTNEWMERGEONLY followed by tree reconstruction
.TP
\fB\-rcluster\fR <percent>
Percentage of partition pairs (relaxed clustering alg.)
.TP
\fB\-mset\fR program
Restrict search to models supported by other programs
(i.e., raxml, phyml or mrbayes)
.TP
\fB\-mset\fR m1,...,mk
Restrict search to models in a comma\-separated list
(e.g. \fB\-mset\fR WAG,LG,JTT)
.TP
\fB\-msub\fR source
Restrict search to AA models designed for specific sources
(i.e., nuclear, mitochondrial, chloroplast or viral)
.TP
\fB\-mfreq\fR f1,...,fk
Restrict search to using a list of state frequencies
(default protein: \fB\-mfreq\fR FU,F; codon: \fB\-mfreq\fR ,F1x4,F3x4,F)
.TP
\fB\-mrate\fR r1,...,rk
Restrict search to using a list of rate\-across\-sites models
(e.g. \fB\-mrate\fR E,I,G,I+G,R)
.TP
\fB\-cmin\fR <kmin>
Min #categories for FreeRate model [+R] (default: 2)
.TP
\fB\-cmax\fR <kmax>
Max #categories for FreeRate model [+R] (default: 10)
.TP
???merit AIC|AICc|BIC
Optimality criterion to use (default: all)
.TP
\fB\-mtree\fR
Performing full tree search for each model considered
.TP
\fB\-mredo\fR
Ignoring model results computed earlier (default: no)
.TP
\fB\-madd\fR mx1,...,mxk
List of mixture models to also consider
.TP
\fB\-mdef\fR <nexus_file>
A model definition NEXUS file (see Manual)
.SS "SUBSTITUTION MODEL:"
.HP
\fB\-m\fR <model_name>
.TP
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)
.TP
Protein: LG (default), Poisson, cpREV, mtREV, Dayhoff, mtMAM,
JTT, WAG, mtART, mtZOA, VT, rtREV, DCMut, PMB, HIVb,
HIVw, JTTDCMut, FLU, Blosum62, GTR20
.TP
Protein mixture: C10,...,C60, EX2, EX3, EHO, UL2, UL3, EX_EHO, LG4M, LG4X,
JTTCF4G
.IP
Binary: JC2 (default), GTR2
.IP
Empirical codon: KOSI07, SCHN05
.TP
Mechanistic codon: GY (default), MG, MGK, GY0K, GY1KTS, GY1KTV, GY2K,
MG1KTS, MG1KTV, MG2K
.IP
Semi\-empirical codon: XX_YY where XX is empirical and YY is mechanistic model
.IP
Morphology/SNP: MK (default), ORDERED
.TP
Otherwise: Name of file containing user\-model parameters
(rate parameters and state frequencies)
.TP
\fB\-m\fR <model_name>+F or +FO or +FU or +FQ (default: auto)
counted, optimized, user\-defined, equal state frequency
.TP
\fB\-m\fR <model_name>+F1x4 or +F3x4
Codon frequencies
.TP
\fB\-m\fR <model_name>+ASC
Ascertainment bias correction for morphological/SNP data
.TP
\fB\-m\fR "MIX{m1,...mK}"
Mixture model with K components
.TP
\fB\-m\fR "FMIX{f1,...fK}"
Frequency mixture model with K components
.TP
\fB\-mwopt\fR
Turn on optimizing mixture weights (default: none)
.SS "RATE HETEROGENEITY AMONG SITES:"
.TP
\fB\-m\fR <model_name>+I or +G[n] or +I+G[n] or +R[n]
Invar, Gamma, Invar+Gamma, or FreeRate model where 'n' is
number of categories (default: n=4)
.TP
\fB\-a\fR <Gamma_shape>
Gamma shape parameter for site rates (default: estimate)
.TP
\fB\-amin\fR <min_shape>
Min Gamma shape parameter for site rates (default: 0.02)
.TP
\fB\-gmedian\fR
Median approximation for +G site rates (default: mean)
.TP
\fB\-\-opt\-gamma\-inv\fR
More thorough estimation for +I+G model parameters
.TP
\fB\-i\fR <p_invar>
Proportion of invariable sites (default: estimate)
.TP
\fB\-wsr\fR
Write site rates to .rate file
.TP
\fB\-mh\fR
Computing site\-specific rates to .mhrate file using
Meyer & von Haeseler (2003) method
.SS "SITE-SPECIFIC FREQUENCY MODEL:"
.TP
\fB\-ft\fR <tree_file>
Input tree to infer site frequency model
.TP
\fB\-fs\fR <in_freq_file>
Input site frequency model file
.TP
\fB\-fmax\fR
Posterior maximum instead of posterior mean approximation
.SS "CONSENSUS RECONSTRUCTION:"
.TP
\fB\-t\fR <tree_file>
Set of input trees for consensus reconstruction
.TP
\fB\-minsup\fR <threshold>
Min split support in range [0,1]; 0.5 for majority\-rule
consensus (default: 0, i.e. extended consensus)
.TP
\fB\-bi\fR <burnin>
Discarding <burnin> trees at beginning of <treefile>
.TP
\fB\-con\fR
Computing consensus tree to .contree file
.TP
\fB\-net\fR
Computing consensus network to .nex file
.TP
\fB\-sup\fR <target_tree>
Assigning support values for <target_tree> to .suptree
.TP
\fB\-suptag\fR <name>
Node name (or ALL) to assign tree IDs where node occurs
.SS "ROBINSON-FOULDS DISTANCE:"
.TP
\fB\-rf_all\fR
Computing all\-to\-all RF distances of trees in <treefile>
.TP
\fB\-rf\fR <treefile2>
Computing all RF distances between two sets of trees
stored in <treefile> and <treefile2>
.TP
\fB\-rf_adj\fR
Computing RF distances of adjacent trees in <treefile>
.SS "TREE TOPOLOGY TEST:"
.TP
\fB\-z\fR <trees_file>
Evaluating a set of user trees
.TP
\fB\-zb\fR <#replicates>
Performing BP,KH,SH,ELW tests for trees passed via \fB\-z\fR
.TP
\fB\-zw\fR
Also performing weighted\-KH and weighted\-SH tests
.TP
\fB\-au\fR
Also performing approximately unbiased (AU) test
.SS "GENERATING RANDOM TREES:"
.TP
\fB\-r\fR <num_taxa>
Create a random tree under Yule\-Harding model
.TP
\fB\-ru\fR <num_taxa>
Create a random tree under Uniform model
.TP
\fB\-rcat\fR <num_taxa>
Create a random caterpillar tree
.TP
\fB\-rbal\fR <num_taxa>
Create a random balanced tree
.TP
\fB\-rcsg\fR <num_taxa>
Create a random circular split network
.TP
\fB\-rlen\fR <min_len> <mean_len> <max_len>
min, mean, and max branch lengths of random trees
.SS "MISCELLANEOUS:"
.TP
\fB\-wt\fR
Write locally optimal trees into .treels file
.TP
\fB\-blfix\fR
Fix branch lengths of user tree passed via \fB\-te\fR
.TP
\fB\-blscale\fR
Scale branch lengths of user tree passed via \fB\-t\fR
.TP
\fB\-blmin\fR
Min branch length for optimization (default 0.000001)
.TP
\fB\-blmax\fR
Max branch length for optimization (default 100)
.TP
\fB\-wsr\fR
Write site rates and categories to .rate file
.TP
\fB\-wsl\fR
Write site log\-likelihoods to .sitelh file
.TP
\fB\-wslr\fR
Write site log\-likelihoods per rate category
.TP
\fB\-wslm\fR
Write site log\-likelihoods per mixture class
.TP
\fB\-wslmr\fR
Write site log\-likelihoods per mixture+rate class
.TP
\fB\-wspr\fR
Write site probabilities per rate category
.TP
\fB\-wspm\fR
Write site probabilities per mixture class
.TP
\fB\-wspmr\fR
Write site probabilities per mixture+rate class
.TP
\fB\-wpl\fR
Write partition log\-likelihoods to .partlh file
.TP
\fB\-fconst\fR f1,...,fN
Add constant patterns into alignment (N=#nstates)
.TP
\fB\-me\fR <epsilon>
Logl epsilon for model parameter optimization (default 0.01)
.TP
\fB\-\-no\-outfiles\fR
Suppress printing output files