man iqtree (1): efficient phylogenetic software by maximum likelihood

SYNOPSIS

iqtree ,-s <alignment> /[,OPTIONS/]

DESCRIPTION

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> 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>: 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
-keep-ident: Keep identical sequences (default: remove & finally add)

CHECKPOINTING TO RESUME STOPPED RUN:

-redo: Redo analysis even for successful runs (default: resume)
-cptime <seconds>: Minimum checkpoint time interval (default: 20)

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:

-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: 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)
-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
-au: Also performing approximately unbiased (AU) test

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)

SYNOPSIS

DESCRIPTION

GENERAL OPTIONS:

CHECKPOINTING TO RESUME STOPPED RUN:

LIKELIHOOD MAPPING ANALYSIS:

NEW STOCHASTIC TREE SEARCH ALGORITHM:

ULTRAFAST BOOTSTRAP:

STANDARD NON-PARAMETRIC BOOTSTRAP:

SINGLE BRANCH TEST:

AUTOMATIC MODEL SELECTION:

SUBSTITUTION MODEL:

RATE HETEROGENEITY:

TEST OF MODEL HOMOGENEITY:

CONSENSUS RECONSTRUCTION:

ROBINSON-FOULDS DISTANCE:

TREE TOPOLOGY TEST:

GENERATING RANDOM TREES:

MISCELLANEOUS:

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