.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
.TH IQTREE-MPI "1" "December 2019" "iqtree-mpi 1.6.12+dfsg" "User Commands"
.SH NAME
iqtree-mpi \- efficient phylogenetic software by maximum likelihood (multiprocessor version)
.SH SYNOPSIS
.B iqtree-mpi
\fI\,-s <alignment> \/\fR[\fI\,OPTIONS\/\fR]
.SH 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.
.SS "GENERAL OPTIONS:"
.TP
\-? or \fB\-h\fR
Print this help dialog
.TP
\fB\-version\fR
Display version number
.TP
\fB\-s\fR <alignment>
Input alignment in PHYLIP/FASTA/NEXUS/CLUSTAL/MSF format
.TP
\fB\-st\fR <data_type>
BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto\-detect)
.TP
\fB\-q\fR <partition_file>
Edge\-linked partition model (file in NEXUS/RAxML format)
.HP
\fB\-spp\fR <partition_file> Like \fB\-q\fR option but allowing partition\-specific rates
.HP
\fB\-sp\fR <partition_file> Edge\-unlinked partition model (like \fB\-M\fR option of RAxML)
.TP
\fB\-t\fR <start_tree_file> or \fB\-t\fR BIONJ or \fB\-t\fR RANDOM
Starting tree (default: 99 parsimony tree and BIONJ)
.HP
\fB\-te\fR <user_tree_file> Like \fB\-t\fR but fixing user tree (no tree search performed)
.TP
\fB\-o\fR <outgroup_taxon>
Outgroup taxon name for writing .treefile
.TP
\fB\-pre\fR <PREFIX>
Prefix for all output files (default: aln/partition)
.TP
\fB\-nt\fR <num_threads>
Number of cores/threads or AUTO for automatic detection
.HP
\fB\-ntmax\fR <max_threads> Max number of threads by \fB\-nt\fR AUTO (default: #CPU cores)
.TP
\fB\-seed\fR <number>
Random seed number, normally used for debugging purpose
.TP
\fB\-v\fR, \fB\-vv\fR, \fB\-vvv\fR
Verbose mode, printing more messages to screen
.TP
\fB\-quiet\fR
Quiet mode, suppress printing to screen (stdout)
.TP
\fB\-keep\-ident\fR
Keep identical sequences (default: remove & finally add)
.TP
\fB\-safe\fR
Safe likelihood kernel to avoid numerical underflow
.TP
\fB\-mem\fR RAM
Maximal RAM usage for memory saving mode
.TP
\fB\-\-runs\fR NUMBER
Number of indepedent runs (default: 1)
.SS "CHECKPOINTING TO RESUME STOPPED RUN:"
.TP
\fB\-redo\fR
Redo analysis even for successful runs (default: resume)
.TP
\fB\-cptime\fR <seconds>
Minimum checkpoint time interval (default: 60 sec)
.SS "LIKELIHOOD MAPPING ANALYSIS:"
.TP
\fB\-lmap\fR <#quartets>
Number of quartets for likelihood mapping analysis
.HP
\fB\-lmclust\fR <clustfile> NEXUS file containing clusters for likelihood mapping
.TP
\fB\-wql\fR
Print quartet log\-likelihoods to .quartetlh file
.SS "NEW STOCHASTIC TREE SEARCH ALGORITHM:"
.TP
\fB\-ninit\fR <number>
Number of initial parsimony trees (default: 100)
.TP
\fB\-ntop\fR <number>
Number of top initial trees (default: 20)
.TP
\fB\-nbest\fR <number>
Number of best trees retained during search (defaut: 5)
.TP
\fB\-n\fR <#iterations>
Fix number of iterations to stop (default: auto)
.TP
\fB\-nstop\fR <number>
Number of unsuccessful iterations to stop (default: 100)
.TP
\fB\-pers\fR <proportion>
Perturbation strength for randomized NNI (default: 0.5)
.TP
\fB\-sprrad\fR <number>
Radius for parsimony SPR search (default: 6)
.TP
\fB\-allnni\fR
Perform more thorough NNI search (default: off)
.HP
\fB\-g\fR <constraint_tree> (Multifurcating) topological constraint tree file
.TP
\fB\-fast\fR
Fast search to resemble FastTree
.SS "ULTRAFAST BOOTSTRAP:"
.TP
\fB\-bb\fR <#replicates>
Ultrafast bootstrap (>=1000)
.TP
\fB\-bsam\fR GENE|GENESITE
Resample GENE or GENE+SITE for partition (default: SITE)
.TP
\fB\-wbt\fR
Write bootstrap trees to .ufboot file (default: none)
.TP
\fB\-wbtl\fR
Like \fB\-wbt\fR but also writing branch lengths
.TP
\fB\-nm\fR <#iterations>
Maximum number of iterations (default: 1000)
.HP
\fB\-nstep\fR <#iterations> #Iterations for UFBoot stopping rule (default: 100)
.TP
\fB\-bcor\fR <min_corr>
Minimum correlation coefficient (default: 0.99)
.TP
\fB\-beps\fR <epsilon>
RELL epsilon to break tie (default: 0.5)
.TP
\fB\-bnni\fR
Optimize UFBoot trees by NNI on bootstrap alignment
.TP
\fB\-j\fR <jackknife>
Proportion of sites for jackknife (default: NONE)
.SS "STANDARD NON-PARAMETRIC BOOTSTRAP:"
.TP
\fB\-b\fR <#replicates>
Bootstrap + ML tree + consensus tree (>=100)
.TP
\fB\-bc\fR <#replicates>
Bootstrap + consensus tree
.TP
\fB\-bo\fR <#replicates>
Bootstrap only
.SS "SINGLE BRANCH TEST:"
.TP
\fB\-alrt\fR <#replicates>
SH\-like approximate likelihood ratio test (SH\-aLRT)
.TP
\fB\-alrt\fR 0
Parametric aLRT test (Anisimova and Gascuel 2006)
.TP
\fB\-abayes\fR
approximate Bayes test (Anisimova et al. 2011)
.TP
\fB\-lbp\fR <#replicates>
Fast local bootstrap probabilities
.SS "MODEL-FINDER:"
.TP
\fB\-m\fR TESTONLY
Standard model selection (like jModelTest, ProtTest)
.TP
\fB\-m\fR TEST
Standard model selection followed by tree inference
.TP
\fB\-m\fR MF
Extended model selection with FreeRate heterogeneity
.TP
\fB\-m\fR MFP
Extended model selection followed by tree inference
.TP
\fB\-m\fR TESTMERGEONLY
Find best partition scheme (like PartitionFinder)
.TP
\fB\-m\fR TESTMERGE
Find best partition scheme followed by tree inference
.TP
\fB\-m\fR MF+MERGE
Find best partition scheme incl. FreeRate heterogeneity
.TP
\fB\-m\fR MFP+MERGE
Like \fB\-m\fR MF+MERGE followed by tree inference
.TP
\fB\-rcluster\fR <percent>
Percentage of partition pairs (relaxed clustering alg.)
.TP
\fB\-rclusterf\fR <perc.>
Percentage of partition pairs (fast relaxed clustering)
.TP
\fB\-rcluster\-max\fR <num>
Max number of partition pairs (default: 10*#partitions)
.TP
\fB\-mset\fR program
Restrict search to models supported by other programs
(raxml, phyml or mrbayes)
.TP
\fB\-mset\fR <lm\-subset>
Restrict search to a subset of the Lie\-Markov models
Options for lm\-subset are:
liemarkov, liemarkovry, liemarkovws, liemarkovmk, strandsymmetric
.TP
\fB\-mset\fR m1,...,mk
Restrict search to models in a comma\-separated list
(e.g. \fB\-mset\fR WAG,LG,JTT)
.TP
\fB\-msub\fR source
Restrict search to AA models for specific sources
(nuclear, mitochondrial, chloroplast or viral)
.TP
\fB\-mfreq\fR f1,...,fk
Restrict search to using a list of state frequencies
(default AA: \fB\-mfreq\fR FU,F; codon: \fB\-mfreq\fR ,F1x4,F3x4,F)
.TP
\fB\-mrate\fR r1,...,rk
Restrict search to a list of rate\-across\-sites models
(e.g. \fB\-mrate\fR E,I,G,I+G,R is used for \fB\-m\fR MF)
.TP
\fB\-cmin\fR <kmin>
Min #categories for FreeRate model [+R] (default: 2)
.TP
\fB\-cmax\fR <kmax>
Max #categories for FreeRate model [+R] (default: 10)
.TP
\fB\-merit\fR AIC|AICc|BIC
Optimality criterion to use (default: all)
.TP
\fB\-mtree\fR
Perform full tree search for each model considered
.TP
\fB\-mredo\fR
Ignore model results computed earlier (default: reuse)
.TP
\fB\-madd\fR mx1,...,mxk
List of mixture models to also consider
.TP
\fB\-mdef\fR <nexus_file>
A model definition NEXUS file (see Manual)
.SS "SUBSTITUTION MODEL:"
.HP
\fB\-m\fR <model_name>
.TP
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)
.TP
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
.IP
Protein mixture: C10,...,C60, EX2, EX3, EHO, UL2, UL3, EX_EHO, LG4M, LG4X
.IP
Binary: JC2 (default), GTR2
.IP
Empirical codon: KOSI07, SCHN05
.TP
Mechanistic codon: GY (default), MG, MGK, GY0K, GY1KTS, GY1KTV, GY2K,
MG1KTS, MG1KTV, MG2K
.IP
Semi\-empirical codon: XX_YY where XX is empirical and YY is mechanistic model
.IP
Morphology/SNP: MK (default), ORDERED, GTR
Lie Markov DNA: One of the following, optionally prefixed by RY, WS or MK:
.TP
1.1,
2.2b, 3.3a, 3.3b,  3.3c,
.TP
3.4,
4.4a, 4.4b, 4.5a,  4.5b,
.TP
5.6a, 5.6b, 5.7a, 5.7b,
5.7c,
.TP
5.11a,5.11b,5.11c,5.16,
6.6,
.TP
6.7a, 6.7b, 6.8a, 6.8b,
6.17a,
.TP
6.17b,8.8,
8.10a,8.10b, 8.16,
.TP
8.17, 8.18, 9.20a,9.20b,10.12,
10.34,12.12
.IP
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.
.IP
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 \fB\-optfromgiven\fR option supplied)
.IP
Otherwise: Name of file containing user\-model parameters
.IP
(rate parameters and state frequencies)
.SS "STATE FREQUENCY:"
.IP
Append one of the following +F... to \fB\-m\fR <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),
.IP
+FWS is freq(A+T)=1/2=freq(C+G), +FMK is freq(A+C)=1/2=freq(G+T).
.TP
+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).
.TP
+FU
Amino\-acid frequencies by the given protein matrix
.TP
+F1x4 (codon model)
Equal NT frequencies over three codon positions
.TP
+F3x4 (codon model)
Unequal NT frequencies over three codon positions
.SS "MIXTURE MODEL:"
.TP
\fB\-m\fR "MIX{model1,...,modelK}"
Mixture model with K components
.TP
\fB\-m\fR "FMIX{freq1,...freqK}"
Frequency mixture model with K components
.TP
\fB\-mwopt\fR
Turn on optimizing mixture weights (default: none)
.SS "RATE HETEROGENEITY AMONG SITES:"
.TP
\fB\-m\fR modelname+I
A proportion of invariable sites
.TP
\fB\-m\fR modelname+G[n]
Discrete Gamma model with n categories (default n=4)
.TP
\fB\-m\fR modelname*G[n]
Discrete Gamma model with unlinked model parameters
.TP
\fB\-m\fR modelname+I+G[n]
Invariable sites plus Gamma model with n categories
.TP
\fB\-m\fR modelname+R[n]
FreeRate model with n categories (default n=4)
.TP
\fB\-m\fR modelname*R[n]
FreeRate model with unlinked model parameters
.TP
\fB\-m\fR modelname+I+R[n]
Invariable sites plus FreeRate model with n categories
.TP
\fB\-m\fR modelname+Hn
Heterotachy model with n classes
.TP
\fB\-m\fR modelname*Hn
Heterotachy model with n classes and unlinked parameters
.TP
\fB\-a\fR <Gamma_shape>
Gamma shape parameter for site rates (default: estimate)
.TP
\fB\-amin\fR <min_shape>
Min Gamma shape parameter for site rates (default: 0.02)
.TP
\fB\-gmedian\fR
Median approximation for +G site rates (default: mean)
.TP
\fB\-\-opt\-gamma\-inv\fR
More thorough estimation for +I+G model parameters
.TP
\fB\-i\fR <p_invar>
Proportion of invariable sites (default: estimate)
.TP
\fB\-wsr\fR
Write site rates to .rate file
.TP
\fB\-mh\fR
Computing site\-specific rates to .mhrate file using
Meyer & von Haeseler (2003) method
.SS "POLYMORPHISM AWARE MODELS (PoMo):"
.TP
\fB\-s\fR <counts_file>
Input counts file (see manual)
.TP
\fB\-m\fR <MODEL>+P
DNA substitution model (see above) used with PoMo
.TP
+N<POPSIZE>
Virtual population size (default: 9)
.TP
+[WB|WH|S]
Sampling method (default: +WB), WB: Weighted binomial,
WH: Weighted hypergeometric S: Sampled sampling
.TP
+G[n]
Discrete Gamma rate model with n categories (default n=4)
.SS "ASCERTAINMENT BIAS CORRECTION:"
.TP
\fB\-m\fR modelname+ASC
Correction for absence of invariant sites in alignment
.SS "SINGLE TOPOLOGY HETEROTACHY MODEL:"
.TP
\fB\-m\fR <model_name>+H[k]
Heterotachy model mixed branch lengths with k classes
.HP
\fB\-m\fR "MIX{m1,...mK}+H"
.TP
\fB\-nni\-eval\fR <m>
Loop m times for NNI evaluation (default m=1)
.SS "SITE-SPECIFIC FREQUENCY MODEL:"
.TP
\fB\-ft\fR <tree_file>
Input tree to infer site frequency model
.TP
\fB\-fs\fR <in_freq_file>
Input site frequency model file
.TP
\fB\-fmax\fR
Posterior maximum instead of mean approximation
.SS "CONSENSUS RECONSTRUCTION:"
.TP
\fB\-t\fR <tree_file>
Set of input trees for consensus reconstruction
.TP
\fB\-minsup\fR <threshold>
Min split support in range [0,1]; 0.5 for majority\-rule
consensus (default: 0, i.e. extended consensus)
.TP
\fB\-bi\fR <burnin>
Discarding <burnin> trees at beginning of <treefile>
.TP
\fB\-con\fR
Computing consensus tree to .contree file
.TP
\fB\-net\fR
Computing consensus network to .nex file
.TP
\fB\-sup\fR <target_tree>
Assigning support values for <target_tree> to .suptree
.TP
\fB\-suptag\fR <name>
Node name (or ALL) to assign tree IDs where node occurs
.SS "ROBINSON-FOULDS DISTANCE:"
.TP
\fB\-rf_all\fR
Computing all\-to\-all RF distances of trees in <treefile>
.TP
\fB\-rf\fR <treefile2>
Computing all RF distances between two sets of trees
stored in <treefile> and <treefile2>
.TP
\fB\-rf_adj\fR
Computing RF distances of adjacent trees in <treefile>
.SS "TREE TOPOLOGY TEST:"
.TP
\fB\-z\fR <trees_file>
Evaluating a set of user trees
.TP
\fB\-zb\fR <#replicates>
Performing BP,KH,SH,ELW tests for trees passed via \fB\-z\fR
.TP
\fB\-zw\fR
Also performing weighted\-KH and weighted\-SH tests
.TP
\fB\-au\fR
Also performing approximately unbiased (AU) test
.SS "ANCESTRAL STATE RECONSTRUCTION:"
.TP
\fB\-asr\fR
Ancestral state reconstruction by empirical Bayes
.TP
\fB\-asr\-min\fR <prob>
Min probability of ancestral state (default: equil freq)
.SS "GENERATING RANDOM TREES:"
.TP
\fB\-r\fR <num_taxa>
Create a random tree under Yule\-Harding model
.TP
\fB\-ru\fR <num_taxa>
Create a random tree under Uniform model
.TP
\fB\-rcat\fR <num_taxa>
Create a random caterpillar tree
.TP
\fB\-rbal\fR <num_taxa>
Create a random balanced tree
.TP
\fB\-rcsg\fR <num_taxa>
Create a random circular split network
.TP
\fB\-rlen\fR <min_len> <mean_len> <max_len>
min, mean, and max branch lengths of random trees
.SS "MISCELLANEOUS:"
.TP
\fB\-wt\fR
Write locally optimal trees into .treels file
.TP
\fB\-blfix\fR
Fix branch lengths of user tree passed via \fB\-te\fR
.TP
\fB\-blscale\fR
Scale branch lengths of user tree passed via \fB\-t\fR
.TP
\fB\-blmin\fR
Min branch length for optimization (default 0.000001)
.TP
\fB\-blmax\fR
Max branch length for optimization (default 100)
.TP
\fB\-wsr\fR
Write site rates and categories to .rate file
.TP
\fB\-wsl\fR
Write site log\-likelihoods to .sitelh file
.TP
\fB\-wslr\fR
Write site log\-likelihoods per rate category
.TP
\fB\-wslm\fR
Write site log\-likelihoods per mixture class
.TP
\fB\-wslmr\fR
Write site log\-likelihoods per mixture+rate class
.TP
\fB\-wspr\fR
Write site probabilities per rate category
.TP
\fB\-wspm\fR
Write site probabilities per mixture class
.TP
\fB\-wspmr\fR
Write site probabilities per mixture+rate class
.TP
\fB\-wpl\fR
Write partition log\-likelihoods to .partlh file
.TP
\fB\-fconst\fR f1,...,fN
Add constant patterns into alignment (N=#nstates)
.TP
\fB\-me\fR <epsilon>
LogL epsilon for parameter estimation (default 0.01)
.TP
\fB\-\-no\-outfiles\fR
Suppress printing output files
.TP
\fB\-\-eigenlib\fR
Use Eigen3 library
.TP
\fB\-alninfo\fR
Print alignment sites statistics to .alninfo
.TP
\fB\-czb\fR
Collapse zero branches in final tree
.TP
\fB\-\-show\-lh\fR
Compute tree likelihood without optimisation