iqtree-omp - efficient phylogenetic software by maximum likelihood
(multiprocessor version)
iqtree-omp -s <alignment> [OPTIONS]
IQ-TREE multicore version 1.6.12 for Linux 64-bit built Dec 4 2019
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt,
Dominik Schrempf, Michael Woodhams.
- -? 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)
- -redo
- Redo analysis even for successful runs (default: resume)
- -cptime
<seconds>
- Minimum checkpoint time interval (default: 60 sec)
- -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
- -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
- -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)
- -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)
-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)
- 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
- -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)
- -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
- -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>
- -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
- -asr
- Ancestral state reconstruction by empirical Bayes
- -asr-min
<prob>
- Min probability of ancestral state (default: equil freq)
- -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