.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH IQTREE2 "1" "March 2024" "iqtree2 2.0.7+dfsg" "User Commands"
.SH NAME
iqtree2 \- efficient phylogenetic software by maximum likelihood
.SH SYNOPSIS
.B iqtree
[\fI\,-s ALIGNMENT\/\fR] [\fI\,-p PARTITION\/\fR] [\fI\,-m MODEL\/\fR] [\fI\,-t TREE\/\fR] ...
.SH DESCRIPTION
IQ\-TREE multicore version 2.0.7 for Linux 64\-bit built Mar 25 2024
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
.SS "GENERAL OPTIONS:"
.TP
\fB\-h\fR, \fB\-\-help\fR
Print (more) help usages
.TP
\fB\-s\fR FILE[,...,FILE]
PHYLIP/FASTA/NEXUS/CLUSTAL/MSF alignment file(s)
.TP
\fB\-s\fR DIR
Directory of alignment files
.TP
\fB\-\-seqtype\fR STRING
BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto\-detect)
.TP
\fB\-t\fR FILE|PARS|RAND
Starting tree (default: 99 parsimony and BIONJ)
.TP
\fB\-o\fR TAX[,...,TAX]
Outgroup taxon (list) for writing .treefile
.TP
\fB\-\-prefix\fR STRING
Prefix for all output files (default: aln/partition)
.TP
\fB\-\-seed\fR NUM
Random seed number, normally used for debugging purpose
.TP
\fB\-\-safe\fR
Safe likelihood kernel to avoid numerical underflow
.TP
\fB\-\-mem\fR NUM[G|M|%]
Maximal RAM usage in GB | MB | %
.TP
\fB\-\-runs\fR NUM
Number of indepedent runs (default: 1)
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Verbose mode, printing more messages to screen
.TP
\fB\-V\fR, \fB\-\-version\fR
Display version number
.TP
\fB\-\-quiet\fR
Quiet mode, suppress printing to screen (stdout)
.TP
\fB\-fconst\fR f1,...,fN
Add constant patterns into alignment (N=no. states)
.TP
\fB\-\-epsilon\fR NUM
Likelihood epsilon for parameter estimate (default 0.01)
.TP
\fB\-T\fR NUM|AUTO
No. cores/threads or AUTO\-detect (default: 1)
.TP
\fB\-\-threads\-max\fR NUM
Max number of threads for \fB\-T\fR AUTO (default: all cores)
.SS "CHECKPOINT:"
.TP
\fB\-\-redo\fR
Redo both ModelFinder and tree search
.TP
\fB\-\-redo\-tree\fR
Restore ModelFinder and only redo tree search
.TP
\fB\-\-undo\fR
Revoke finished run, used when changing some options
.TP
\fB\-\-cptime\fR NUM
Minimum checkpoint interval (default: 60 sec and adapt)
.SS "PARTITION MODEL:"
.TP
\fB\-p\fR FILE|DIR
NEXUS/RAxML partition file or directory with alignments
Edge\-linked proportional partition model
.TP
\fB\-q\fR FILE|DIR
Like \fB\-p\fR but edge\-linked equal partition model
.TP
\fB\-Q\fR FILE|DIR
Like \fB\-p\fR but edge\-unlinked partition model
.TP
\fB\-S\fR FILE|DIR
Like \fB\-p\fR but separate tree inference
.TP
\fB\-\-subsample\fR NUM
Randomly sub\-sample partitions (negative for complement)
.HP
\fB\-\-subsample\-seed\fR NUM Random number seed for \fB\-\-subsample\fR
.SS "LIKELIHOOD/QUARTET MAPPING:"
.TP
\fB\-\-lmap\fR NUM
Number of quartets for likelihood mapping analysis
.TP
\fB\-\-lmclust\fR FILE
NEXUS file containing clusters for likelihood mapping
.TP
\fB\-\-quartetlh\fR
Print quartet log\-likelihoods to .quartetlh file
.SS "TREE SEARCH ALGORITHM:"
.TP
\fB\-\-ninit\fR NUM
Number of initial parsimony trees (default: 100)
.TP
\fB\-\-ntop\fR NUM
Number of top initial trees (default: 20)
.TP
\fB\-\-nbest\fR NUM
Number of best trees retained during search (defaut: 5)
.TP
\fB\-n\fR NUM
Fix number of iterations to stop (default: OFF)
.TP
\fB\-\-nstop\fR NUM
Number of unsuccessful iterations to stop (default: 100)
.TP
\fB\-\-perturb\fR NUM
Perturbation strength for randomized NNI (default: 0.5)
.TP
\fB\-\-radius\fR NUM
Radius for parsimony SPR search (default: 6)
.TP
\fB\-\-allnni\fR
Perform more thorough NNI search (default: OFF)
.TP
\fB\-g\fR FILE
(Multifurcating) topological constraint tree file
.TP
\fB\-\-fast\fR
Fast search to resemble FastTree
.TP
\fB\-\-polytomy\fR
Collapse near\-zero branches into polytomy
.TP
\fB\-\-tree\-fix\fR
Fix \fB\-t\fR tree (no tree search performed)
.TP
\fB\-\-treels\fR
Write locally optimal trees into .treels file
.TP
\fB\-\-show\-lh\fR
Compute tree likelihood without optimisation
.TP
\fB\-\-terrace\fR
Check if the tree lies on a phylogenetic terrace
.SS "ULTRAFAST BOOTSTRAP/JACKKNIFE:"
.TP
\fB\-B\fR, \fB\-\-ufboot\fR NUM
Replicates for ultrafast bootstrap (>=1000)
.TP
\fB\-J\fR, \fB\-\-ufjack\fR NUM
Replicates for ultrafast jackknife (>=1000)
.TP
\fB\-\-jack\-prop\fR NUM
Subsampling proportion for jackknife (default: 0.5)
.TP
\fB\-\-sampling\fR STRING
GENE|GENESITE resampling for partitions (default: SITE)
.TP
\fB\-\-boot\-trees\fR
Write bootstrap trees to .ufboot file (default: none)
.TP
\fB\-\-wbtl\fR
Like \fB\-\-boot\-trees\fR but also writing branch lengths
.TP
\fB\-\-nmax\fR NUM
Maximum number of iterations (default: 1000)
.TP
\fB\-\-nstep\fR NUM
Iterations for UFBoot stopping rule (default: 100)
.TP
\fB\-\-bcor\fR NUM
Minimum correlation coefficient (default: 0.99)
.TP
\fB\-\-beps\fR NUM
RELL epsilon to break tie (default: 0.5)
.TP
\fB\-\-bnni\fR
Optimize UFBoot trees by NNI on bootstrap alignment
.SS "NON-PARAMETRIC BOOTSTRAP/JACKKNIFE:"
.TP
\fB\-b\fR, \fB\-\-boot\fR NUM
Replicates for bootstrap + ML tree + consensus tree
.TP
\fB\-j\fR, \fB\-\-jack\fR NUM
Replicates for jackknife + ML tree + consensus tree
.TP
\fB\-\-jack\-prop\fR NUM
Subsampling proportion for jackknife (default: 0.5)
.TP
\fB\-\-bcon\fR NUM
Replicates for bootstrap + consensus tree
.TP
\fB\-\-bonly\fR NUM
Replicates for bootstrap only
.TP
\fB\-\-tbe\fR
Transfer bootstrap expectation
.SS "SINGLE BRANCH TEST:"
.TP
\fB\-\-alrt\fR NUM
Replicates for SH approximate likelihood ratio test
.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 NUM
Replicates for 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 ...+LM
Additionally test Lie Markov models
.TP
\fB\-m\fR ...+LMRY
Additionally test Lie Markov models with RY symmetry
.TP
\fB\-m\fR ...+LMWS
Additionally test Lie Markov models with WS symmetry
.TP
\fB\-m\fR ...+LMMK
Additionally test Lie Markov models with MK symmetry
.TP
\fB\-m\fR ...+LMSS
Additionally test strand\-symmetric models
.TP
\fB\-\-mset\fR STRING
Restrict search to models supported by other programs
(raxml, phyml or mrbayes)
.TP
\fB\-\-mset\fR STR,...
Comma\-separated model list (e.g. \fB\-mset\fR WAG,LG,JTT)
.TP
\fB\-\-msub\fR STRING
Amino\-acid model source
(nuclear, mitochondrial, chloroplast or viral)
.TP
\fB\-\-mfreq\fR STR,...
List of state frequencies
.TP
\fB\-\-mrate\fR STR,...
List of rate heterogeneity among sites
(e.g. \fB\-mrate\fR E,I,G,I+G,R is used for \fB\-m\fR MF)
.TP
\fB\-\-cmin\fR NUM
Min categories for FreeRate model [+R] (default: 2)
.TP
\fB\-\-cmax\fR NUM
Max categories for FreeRate model [+R] (default: 10)
.TP
\fB\-\-merit\fR AIC|AICc|BIC
Akaike|Bayesian information criterion (default: BIC)
.TP
\fB\-\-mtree\fR
Perform full tree search for every model
.TP
\fB\-\-madd\fR STR,...
List of mixture models to consider
.TP
\fB\-\-mdef\fR FILE
Model definition NEXUS file (see Manual)
.TP
\fB\-\-modelomatic\fR
Find best codon/protein/DNA models (Whelan et al. 2015)
.SS "PARTITION-FINDER:"
.TP
\fB\-\-merge\fR
Merge partitions to increase model fit
.TP
\fB\-\-merge\fR greedy|rcluster|rclusterf
Set merging algorithm (default: rclusterf)
.TP
\fB\-\-merge\-model\fR 1|all
Use only 1 or all models for merging (default: 1)
.TP
\fB\-\-merge\-model\fR STR,...
Comma\-separated model list for merging
.TP
\fB\-\-merge\-rate\fR 1|all
Use only 1 or all rate heterogeneity (default: 1)
.TP
\fB\-\-merge\-rate\fR STR,...
Comma\-separated rate list for merging
.TP
\fB\-\-rcluster\fR NUM
Percentage of partition pairs for rcluster algorithm
.TP
\fB\-\-rclusterf\fR NUM
Percentage of partition pairs for rclusterf algorithm
.TP
\fB\-\-rcluster\-max\fR NUM
Max number of partition pairs (default: 10*partitions)
.SS "SUBSTITUTION MODEL:"
.TP
\fB\-m\fR STRING
Model name string (e.g. GTR+F+I+G)
.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, FLAVI,
.IP
Q.LG, Q.pfam, Q.pfam_gb, Q.bird, Q.mammal, Q.insect, Q.plant, Q.yeast
.TP
Protein mixture:
C10,...,C60, EX2, EX3, EHO, UL2, UL3, EX_EHO, LG4M, LG4X
.TP
Binary:
JC2 (default), GTR2
.TP
Empirical codon:
KOSI07, SCHN05
.TP
Mechanistic codon:
GY (default), MG, MGK, GY0K, GY1KTS, GY1KTV, GY2K,
MG1KTS, MG1KTV, MG2K
.PP
Semi\-empirical codon:  XX_YY where XX is empirical and YY is mechanistic model
.TP
Morphology/SNP:
MK (default), ORDERED, GTR
.TP
Lie Markov DNA:
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 (optionally prefixed by RY, WS or MK)
.TP
Non\-reversible:
STRSYM (strand symmetric model, equiv. WS6.6),
NONREV, UNREST (unrestricted model, equiv. 12.12)
.TP
Otherwise:
Name of file containing user\-model parameters
.SS "STATE FREQUENCY:"
.TP
\fB\-m\fR ...+F
Empirically counted frequencies from alignment
.TP
\fB\-m\fR ...+FO
Optimized frequencies by maximum\-likelihood
.TP
\fB\-m\fR ...+FQ
Equal frequencies
.TP
\fB\-m\fR ...+FRY
For DNA, freq(A+G)=1/2=freq(C+T)
.TP
\fB\-m\fR ...+FWS
For DNA, freq(A+T)=1/2=freq(C+G)
.TP
\fB\-m\fR ...+FMK
For DNA, freq(A+C)=1/2=freq(G+T)
.TP
\fB\-m\fR ...+Fabcd
4\-digit constraint on ACGT frequency
(e.g. +F1221 means f_A=f_T, f_C=f_G)
.TP
\fB\-m\fR ...+FU
Amino\-acid frequencies given protein matrix
.TP
\fB\-m\fR ...+F1x4
Equal NT frequencies over three codon positions
.TP
\fB\-m\fR ...+F3x4
Unequal NT frequencies over three codon positions
.SS "RATE HETEROGENEITY AMONG SITES:"
.TP
\fB\-m\fR ...+I
A proportion of invariable sites
.TP
\fB\-m\fR ...+G[n]
Discrete Gamma model with n categories (default n=4)
.TP
\fB\-m\fR ...*G[n]
Discrete Gamma model with unlinked model parameters
.TP
\fB\-m\fR ...+I+G[n]
Invariable sites plus Gamma model with n categories
.TP
\fB\-m\fR ...+R[n]
FreeRate model with n categories (default n=4)
.TP
\fB\-m\fR ...*R[n]
FreeRate model with unlinked model parameters
.TP
\fB\-m\fR ...+I+R[n]
Invariable sites plus FreeRate model with n categories
.TP
\fB\-m\fR ...+Hn
Heterotachy model with n classes
.TP
\fB\-m\fR ...*Hn
Heterotachy model with n classes and unlinked parameters
.TP
\fB\-\-alpha\-min\fR NUM
Min Gamma shape parameter for site rates (default: 0.02)
.TP
\fB\-\-gamma\-median\fR
Median approximation for +G site rates (default: mean)
.TP
\fB\-\-rate\fR
Write empirical Bayesian site rates to .rate file
.TP
\fB\-\-mlrate\fR
Write maximum likelihood site rates to .mlrate file
.SS "POLYMORPHISM AWARE MODELS (PoMo):"
.TP
\fB\-s\fR FILE
Input counts file (see manual)
.TP
\fB\-m\fR ...+P
DNA substitution model (see above) used with PoMo
.TP
\fB\-m\fR ...+N<POPSIZE>
Virtual population size (default: 9)
.TP
\fB\-m\fR ...+WB|WH|S]
Weighted binomial sampling
.TP
\fB\-m\fR ...+WH
Weighted hypergeometric sampling
.TP
\fB\-m\fR ...+S
Sampled sampling
.TP
\fB\-m\fR ...+G[n]
Discrete Gamma rate with n categories (default n=4)
.SS "COMPLEX MODELS:"
.TP
\fB\-m\fR "MIX{m1,...,mK}"
Mixture model with K components
.TP
\fB\-m\fR "FMIX{f1,...fK}"
Frequency mixture model with K components
.TP
\fB\-\-mix\-opt\fR
Optimize mixture weights (default: detect)
.TP
\fB\-m\fR ...+ASC
Ascertainment bias correction
.TP
\fB\-\-tree\-freq\fR FILE
Input tree to infer site frequency model
.TP
\fB\-\-site\-freq\fR FILE
Input site frequency model file
.TP
\fB\-\-freq\-max\fR
Posterior maximum instead of mean approximation
.SS "TREE TOPOLOGY TEST:"
.TP
\fB\-\-trees\fR FILE
Set of trees to evaluate log\-likelihoods
.TP
\fB\-\-test\fR NUM
Replicates for topology test
.TP
\fB\-\-test\-weight\fR
Perform weighted KH and SH tests
.TP
\fB\-\-test\-au\fR
Approximately unbiased (AU) test (Shimodaira 2002)
.TP
\fB\-\-sitelh\fR
Write site log\-likelihoods to .sitelh file
.SS "ANCESTRAL STATE RECONSTRUCTION:"
.TP
\fB\-\-ancestral\fR
Ancestral state reconstruction by empirical Bayes
.TP
\fB\-\-asr\-min\fR NUM
Min probability of ancestral state (default: equil freq)
.SS "TEST OF SYMMETRY:"
.TP
\fB\-\-symtest\fR
Perform three tests of symmetry
.TP
\fB\-\-symtest\-only\fR
Do \fB\-\-symtest\fR then exist
.TP
\fB\-\-symtest\-remove\-bad\fR
Do \fB\-\-symtest\fR and remove bad partitions
.TP
\fB\-\-symtest\-remove\-good\fR
Do \fB\-\-symtest\fR and remove good partitions
.TP
\fB\-\-symtest\-type\fR MAR|INT
Use MARginal/INTernal test when removing partitions
.TP
\fB\-\-symtest\-pval\fR NUMER
P\-value cutoff (default: 0.05)
.TP
\fB\-\-symtest\-keep\-zero\fR
Keep NAs in the tests
.SS "CONCORDANCE FACTOR ANALYSIS:"
.TP
\fB\-t\fR FILE
Reference tree to assign concordance factor
.TP
\fB\-\-gcf\fR FILE
Set of source trees for gene concordance factor (gCF)
.TP
\fB\-\-df\-tree\fR
Write discordant trees associated with gDF1
.TP
\fB\-\-scf\fR NUM
Number of quartets for site concordance factor (sCF)
.TP
\fB\-s\fR FILE
Sequence alignment for \fB\-\-scf\fR
.TP
\fB\-p\fR FILE|DIR
Partition file or directory for \fB\-\-scf\fR
.TP
\fB\-\-cf\-verbose\fR
Write CF per tree/locus to cf.stat_tree/_loci
.TP
\fB\-\-cf\-quartet\fR
Write sCF for all resampled quartets to .cf.quartet