table of contents
other versions
- jessie-backports 1.5.3+dfsg-2~bpo8+1
- stretch 1.5.3+dfsg-2
- testing 1.6.8+dfsg-1
- unstable 1.6.9+dfsg-1
IQTREE(1) | User Commands | IQTREE(1) |
NAME¶
iqtree - efficient phylogenetic software by maximum likelihoodSYNOPSIS¶
iqtree -s <alignment> [OPTIONS]DESCRIPTION¶
IQ-TREE version 1.5.3 for Linux 64-bit built Feb 22 2017 Copyright © 2011-2016 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> 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
- -quiet
- Silent 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
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:¶
- -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 <#iterations> (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
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
- Extended model selection incl. 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: LG (default), Poisson, cpREV, mtREV, Dayhoff, mtMAM,
- JTT, WAG, mtART, mtZOA, VT, rtREV, DCMut, PMB, HIVb, HIVw, JTTDCMut, FLU, Blosum62, GTR20
- 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 AMONG SITES:¶
- -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)
- -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
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 posterior 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
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 model parameter optimization (default 0.01)
- --no-outfiles
- Suppress printing output files
February 2017 | iqtree 1.5.3+dfsg |