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IQTREE-MPI(1) User Commands IQTREE-MPI(1)

NAME

iqtree-mpi - efficient phylogenetic software by maximum likelihood (multiprocessor version)

SYNOPSIS

iqtree-mpi -s <alignment> [OPTIONS]

DESCRIPTION

IQ-TREE MPI 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.

GENERAL OPTIONS:

-? or -h
Print this help dialog
Display version number
Input alignment in PHYLIP/FASTA/NEXUS/CLUSTAL/MSF format
BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect)
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)

Starting tree (default: 99 parsimony tree and BIONJ)

-te <user_tree_file> Like -t but fixing user tree (no tree search performed)

Outgroup taxon name for writing .treefile
Prefix for all output files (default: aln/partition)
Number of cores/threads or AUTO for automatic detection

-ntmax <max_threads> Max number of threads by -nt AUTO (default: #CPU cores)

Random seed number, normally used for debugging purpose
Verbose mode, printing more messages to screen
Quiet mode, suppress printing to screen (stdout)
Keep identical sequences (default: remove & finally add)
Safe likelihood kernel to avoid numerical underflow
Maximal RAM usage for memory saving mode
Number of indepedent runs (default: 1)

CHECKPOINTING TO RESUME STOPPED RUN:

Redo analysis even for successful runs (default: resume)
Minimum checkpoint time interval (default: 60 sec)

LIKELIHOOD MAPPING ANALYSIS:

Number of quartets for likelihood mapping analysis

-lmclust <clustfile> NEXUS file containing clusters for likelihood mapping

Print quartet log-likelihoods to .quartetlh file

NEW STOCHASTIC TREE SEARCH ALGORITHM:

Number of initial parsimony trees (default: 100)
Number of top initial trees (default: 20)
Number of best trees retained during search (defaut: 5)
Fix number of iterations to stop (default: auto)
Number of unsuccessful iterations to stop (default: 100)
Perturbation strength for randomized NNI (default: 0.5)
Radius for parsimony SPR search (default: 6)
Perform more thorough NNI search (default: off)

-g <constraint_tree> (Multifurcating) topological constraint tree file

Fast search to resemble FastTree

ULTRAFAST BOOTSTRAP:

Ultrafast bootstrap (>=1000)
Resample GENE or GENE+SITE for partition (default: SITE)
Write bootstrap trees to .ufboot file (default: none)
Like -wbt but also writing branch lengths
Maximum number of iterations (default: 1000)

-nstep <#iterations> #Iterations for UFBoot stopping rule (default: 100)

Minimum correlation coefficient (default: 0.99)
RELL epsilon to break tie (default: 0.5)
Optimize UFBoot trees by NNI on bootstrap alignment
Proportion of sites for jackknife (default: NONE)

STANDARD NON-PARAMETRIC BOOTSTRAP:

Bootstrap + ML tree + consensus tree (>=100)
Bootstrap + consensus tree
Bootstrap only

SINGLE BRANCH TEST:

SH-like approximate likelihood ratio test (SH-aLRT)
Parametric aLRT test (Anisimova and Gascuel 2006)
approximate Bayes test (Anisimova et al. 2011)
Fast local bootstrap probabilities

MODEL-FINDER:

Standard model selection (like jModelTest, ProtTest)
Standard model selection followed by tree inference
Extended model selection with FreeRate heterogeneity
Extended model selection followed by tree inference
Find best partition scheme (like PartitionFinder)
Find best partition scheme followed by tree inference
Find best partition scheme incl. FreeRate heterogeneity
Like -m MF+MERGE followed by tree inference
Percentage of partition pairs (relaxed clustering alg.)
Percentage of partition pairs (fast relaxed clustering)
Max number of partition pairs (default: 10*#partitions)
Restrict search to models supported by other programs (raxml, phyml or mrbayes)
Restrict search to a subset of the Lie-Markov models Options for lm-subset are: liemarkov, liemarkovry, liemarkovws, liemarkovmk, strandsymmetric
Restrict search to models in a comma-separated list (e.g. -mset WAG,LG,JTT)
Restrict search to AA models for specific sources (nuclear, mitochondrial, chloroplast or viral)
Restrict search to using a list of state frequencies (default AA: -mfreq FU,F; codon: -mfreq ,F1x4,F3x4,F)
Restrict search to a list of rate-across-sites models (e.g. -mrate E,I,G,I+G,R is used for -m MF)
Min #categories for FreeRate model [+R] (default: 2)
Max #categories for FreeRate model [+R] (default: 10)
Optimality criterion to use (default: all)
Perform full tree search for each model considered
Ignore model results computed earlier (default: reuse)
List of mixture models to also consider
A model definition NEXUS file (see Manual)

SUBSTITUTION MODEL:

-m <model_name>

TIM, TIMef, TVM, TVMef, SYM, GTR, or 6-digit model specification (e.g., 010010 = HKY)
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
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)

STATE FREQUENCY:

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

MIXTURE MODEL:

Mixture model with K components
Frequency mixture model with K components
Turn on optimizing mixture weights (default: none)

RATE HETEROGENEITY AMONG SITES:

A proportion of invariable sites
Discrete Gamma model with n categories (default n=4)
Discrete Gamma model with unlinked model parameters
Invariable sites plus Gamma model with n categories
FreeRate model with n categories (default n=4)
FreeRate model with unlinked model parameters
Invariable sites plus FreeRate model with n categories
Heterotachy model with n classes
Heterotachy model with n classes and unlinked parameters
Gamma shape parameter for site rates (default: estimate)
Min Gamma shape parameter for site rates (default: 0.02)
Median approximation for +G site rates (default: mean)
More thorough estimation for +I+G model parameters
Proportion of invariable sites (default: estimate)
Write site rates to .rate file
Computing site-specific rates to .mhrate file using Meyer & von Haeseler (2003) method

POLYMORPHISM AWARE MODELS (PoMo):

Input counts file (see manual)
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)

ASCERTAINMENT BIAS CORRECTION:

Correction for absence of invariant sites in alignment

SINGLE TOPOLOGY HETEROTACHY MODEL:

Heterotachy model mixed branch lengths with k classes

-m "MIX{m1,...mK}+H"

Loop m times for NNI evaluation (default m=1)

SITE-SPECIFIC FREQUENCY MODEL:

Input tree to infer site frequency model
Input site frequency model file
Posterior maximum instead of mean approximation

CONSENSUS RECONSTRUCTION:

Set of input trees for consensus reconstruction
Min split support in range [0,1]; 0.5 for majority-rule consensus (default: 0, i.e. extended consensus)
Discarding <burnin> trees at beginning of <treefile>
Computing consensus tree to .contree file
Computing consensus network to .nex file
Assigning support values for <target_tree> to .suptree
Node name (or ALL) to assign tree IDs where node occurs

ROBINSON-FOULDS DISTANCE:

Computing all-to-all RF distances of trees in <treefile>
Computing all RF distances between two sets of trees stored in <treefile> and <treefile2>
Computing RF distances of adjacent trees in <treefile>

TREE TOPOLOGY TEST:

Evaluating a set of user trees
Performing BP,KH,SH,ELW tests for trees passed via -z
Also performing weighted-KH and weighted-SH tests
Also performing approximately unbiased (AU) test

ANCESTRAL STATE RECONSTRUCTION:

Ancestral state reconstruction by empirical Bayes
Min probability of ancestral state (default: equil freq)

GENERATING RANDOM TREES:

Create a random tree under Yule-Harding model
Create a random tree under Uniform model
Create a random caterpillar tree
Create a random balanced tree
Create a random circular split network
min, mean, and max branch lengths of random trees

MISCELLANEOUS:

Write locally optimal trees into .treels file
Fix branch lengths of user tree passed via -te
Scale branch lengths of user tree passed via -t
Min branch length for optimization (default 0.000001)
Max branch length for optimization (default 100)
Write site rates and categories to .rate file
Write site log-likelihoods to .sitelh file
Write site log-likelihoods per rate category
Write site log-likelihoods per mixture class
Write site log-likelihoods per mixture+rate class
Write site probabilities per rate category
Write site probabilities per mixture class
Write site probabilities per mixture+rate class
Write partition log-likelihoods to .partlh file
Add constant patterns into alignment (N=#nstates)
LogL epsilon for parameter estimation (default 0.01)
Suppress printing output files
Use Eigen3 library
Print alignment sites statistics to .alninfo
Collapse zero branches in final tree
Compute tree likelihood without optimisation
December 2019 iqtree-mpi 1.6.12+dfsg