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PROGRAM:

NAME


iqtree - efficient phylogenetic software by maximum likelihood

SYNOPSIS


iqtree -s <alignment> [OPTIONS]

DESCRIPTION


IQ-TREE version 1.3.11.1 for Linux 64-bit built Feb 1 2016 Copyright © 2011-2015 Nguyen
Lam Tung, Olga Chernomor, Arndt von Haeseler and Bui Quang Minh.

GENERAL OPTIONS:
-? or -h
Printing this help dialog

-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> | BIONJ | RANDOM
Starting tree (default: 100 parsimony trees 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>
Using <PREFIX> for output files (default: aln/partition)

-seed <number>
Random seed number, normally used for debugging purpose

-v, -vv, -vvv
Verbose mode, printing more messages to screen

NEW STOCHASTIC TREE SEARCH ALGORITHM:
-pll Use phylogenetic likelihood library (PLL) (default: off)

-numpars <number>
Number of initial parsimony trees (default: 100)

-toppars <number>
Number of best parsimony trees (default: 20)

-sprrad <number>
Radius for parsimony SPR search (default: 6)

-numcand <number>
Size of the candidate tree set (defaut: 5)

-pers <proportion>
Perturbation strength for randomized NNI (default: 0.5)

-allnni
Perform more thorough NNI search (default: off)

-numstop <number>
Number of unsuccessful iterations to stop (default: 100)

-n <#iterations>
Fix number of iterations to <#iterations> (default: auto)

-iqp Use the IQP tree perturbation (default: randomized NNI)

-iqpnni
Switch back to the old IQPNNI tree search algorithm

ULTRAFAST BOOTSTRAP:
-bb <#replicates>
Ultrafast bootstrap (>=1000)

-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)

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

AUTOMATIC MODEL SELECTION:
-m TESTONLY
Standard model selection (like jModelTest, ProtTest)

-m TEST
Like -m TESTONLY but followed by tree reconstruction

-m TESTNEWONLY
New model selection including FreeRate (+R) heterogeneity

-m TESTNEW
Like -m TESTNEWONLY but followed by tree reconstruction

-m TESTMERGEONLY
Select best-fit partition scheme (like PartitionFinder)

-m TESTMERGE
Like -m TESTMERGEONLY but followed by tree reconstruction

-m TESTNEWMERGEONLY
Like -m TESTMERGEONLY but includes FreeRate heterogeneity

-m TESTNEWMERGE
Like -m TESTNEWMERGEONLY followed by tree reconstruction

-rcluster <percent>
Percentage of partition pairs (relaxed clustering alg.)

-mset program
Restrict search to models supported by other programs (i.e., raxml, phyml or
mrbayes)

-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 designed for specific sources (i.e., nuclear,
mitochondrial, chloroplast or viral)

-mfreq f1,...,fk
Restrict search to using a list of state frequencies (default protein: -mfreq FU,F;
codon: -mfreq ,F1x4,F3x4,F)

-mrate r1,...,rk
Restrict search to using a list of rate-across-sites models (e.g. -mrate
E,I,G,I+G,R)

-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 Performing full tree search for each model considered

-mredo Ignoring model results computed earlier (default: no)

-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: WAG (default), Poisson, cpREV, mtREV, Dayhoff, mtMAM,
JTT, LG, mtART, mtZOA, VT, rtREV, DCMut, PMB, HIVb, HIVw, JTTDCMut, FLU, Blosum62

Protein mixture: C10,...,C60, EX2, EX3, EHO, UL2, UL3, EX_EHO, LG4M, LG4X,
JTTCF4G

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

Otherwise: Name of file containing user-model parameters
(rate parameters and state frequencies)

-m <model_name>+F or +FO or +FU or +FQ (default: auto)
counted, optimized, user-defined, equal state frequency

-m <model_name>+F1x4 or +F3x4
Codon frequencies

-m <model_name>+ASC
Ascertainment bias correction for morphological/SNP data

-m "MIX{m1,...mK}"
Mixture model with K components

-m "FMIX{f1,...fK}"
Frequency mixture model with K components

-mwopt Turn on optimizing mixture weights (default: none)

RATE HETEROGENEITY:
-m <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)

-a <Gamma_shape>
Gamma shape parameter for site rates (default: estimate)

-gmedian
Computing mean for Gamma rate category (default: mean)

--test-alpha
More thorough estimation for +I+G model parameters

-i <p_invar>
Proportion of invariable sites (default: estimate)

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

TEST OF MODEL HOMOGENEITY:
-m WHTEST
Testing model (GTR+G) homogeneity assumption using Weiss & von Haeseler (2003)
method

-ns <#simulations>
#Simulations to obtain null-distribution (default: 1000)

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

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

-blmin Min branch length for optimization (default 0.000001)

-blmax Max branch length for optimization (default 100)

-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

-fconst f1,...,fN
Add constant patterns into alignment (N=#nstates)

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