Provided by: iqtree_2.0.7+dfsg-1build2_amd64 
NAME
iqtree2-mpi - efficient phylogenetic software by maximum likelihood (multiprocessor
version)
SYNOPSIS
iqtree [-s ALIGNMENT] [-p PARTITION] [-m MODEL] [-t TREE] ...
DESCRIPTION
IQ-TREE MPI multicore version 2.0.7 for Linux 64-bit built Apr 1 2024 Developed by Bui
Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael
Woodhams.
GENERAL OPTIONS:
-h, --help
Print (more) help usages
-s FILE[,...,FILE]
PHYLIP/FASTA/NEXUS/CLUSTAL/MSF alignment file(s)
-s DIR Directory of alignment files
--seqtype STRING
BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect)
-t FILE|PARS|RAND
Starting tree (default: 99 parsimony and BIONJ)
-o TAX[,...,TAX]
Outgroup taxon (list) for writing .treefile
--prefix STRING
Prefix for all output files (default: aln/partition)
--seed NUM
Random seed number, normally used for debugging purpose
--safe Safe likelihood kernel to avoid numerical underflow
--mem NUM[G|M|%]
Maximal RAM usage in GB | MB | %
--runs NUM
Number of indepedent runs (default: 1)
-v, --verbose
Verbose mode, printing more messages to screen
-V, --version
Display version number
--quiet
Quiet mode, suppress printing to screen (stdout)
-fconst f1,...,fN
Add constant patterns into alignment (N=no. states)
--epsilon NUM
Likelihood epsilon for parameter estimate (default 0.01)
-T NUM|AUTO
No. cores/threads or AUTO-detect (default: 1)
--threads-max NUM
Max number of threads for -T AUTO (default: all cores)
CHECKPOINT:
--redo Redo both ModelFinder and tree search
--redo-tree
Restore ModelFinder and only redo tree search
--undo Revoke finished run, used when changing some options
--cptime NUM
Minimum checkpoint interval (default: 60 sec and adapt)
PARTITION MODEL:
-p FILE|DIR
NEXUS/RAxML partition file or directory with alignments Edge-linked proportional
partition model
-q FILE|DIR
Like -p but edge-linked equal partition model
-Q FILE|DIR
Like -p but edge-unlinked partition model
-S FILE|DIR
Like -p but separate tree inference
--subsample NUM
Randomly sub-sample partitions (negative for complement)
--subsample-seed NUM Random number seed for --subsample
LIKELIHOOD/QUARTET MAPPING:
--lmap NUM
Number of quartets for likelihood mapping analysis
--lmclust FILE
NEXUS file containing clusters for likelihood mapping
--quartetlh
Print quartet log-likelihoods to .quartetlh file
TREE SEARCH ALGORITHM:
--ninit NUM
Number of initial parsimony trees (default: 100)
--ntop NUM
Number of top initial trees (default: 20)
--nbest NUM
Number of best trees retained during search (defaut: 5)
-n NUM Fix number of iterations to stop (default: OFF)
--nstop NUM
Number of unsuccessful iterations to stop (default: 100)
--perturb NUM
Perturbation strength for randomized NNI (default: 0.5)
--radius NUM
Radius for parsimony SPR search (default: 6)
--allnni
Perform more thorough NNI search (default: OFF)
-g FILE
(Multifurcating) topological constraint tree file
--fast Fast search to resemble FastTree
--polytomy
Collapse near-zero branches into polytomy
--tree-fix
Fix -t tree (no tree search performed)
--treels
Write locally optimal trees into .treels file
--show-lh
Compute tree likelihood without optimisation
--terrace
Check if the tree lies on a phylogenetic terrace
ULTRAFAST BOOTSTRAP/JACKKNIFE:
-B, --ufboot NUM
Replicates for ultrafast bootstrap (>=1000)
-J, --ufjack NUM
Replicates for ultrafast jackknife (>=1000)
--jack-prop NUM
Subsampling proportion for jackknife (default: 0.5)
--sampling STRING
GENE|GENESITE resampling for partitions (default: SITE)
--boot-trees
Write bootstrap trees to .ufboot file (default: none)
--wbtl Like --boot-trees but also writing branch lengths
--nmax NUM
Maximum number of iterations (default: 1000)
--nstep NUM
Iterations for UFBoot stopping rule (default: 100)
--bcor NUM
Minimum correlation coefficient (default: 0.99)
--beps NUM
RELL epsilon to break tie (default: 0.5)
--bnni Optimize UFBoot trees by NNI on bootstrap alignment
NON-PARAMETRIC BOOTSTRAP/JACKKNIFE:
-b, --boot NUM
Replicates for bootstrap + ML tree + consensus tree
-j, --jack NUM
Replicates for jackknife + ML tree + consensus tree
--jack-prop NUM
Subsampling proportion for jackknife (default: 0.5)
--bcon NUM
Replicates for bootstrap + consensus tree
--bonly NUM
Replicates for bootstrap only
--tbe Transfer bootstrap expectation
SINGLE BRANCH TEST:
--alrt NUM
Replicates for SH approximate likelihood ratio test
--alrt 0
Parametric aLRT test (Anisimova and Gascuel 2006)
--abayes
approximate Bayes test (Anisimova et al. 2011)
--lbp NUM
Replicates for fast local bootstrap probabilities
MODEL-FINDER:
-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 ...+LM
Additionally test Lie Markov models
-m ...+LMRY
Additionally test Lie Markov models with RY symmetry
-m ...+LMWS
Additionally test Lie Markov models with WS symmetry
-m ...+LMMK
Additionally test Lie Markov models with MK symmetry
-m ...+LMSS
Additionally test strand-symmetric models
--mset STRING
Restrict search to models supported by other programs (raxml, phyml or mrbayes)
--mset STR,...
Comma-separated model list (e.g. -mset WAG,LG,JTT)
--msub STRING
Amino-acid model source (nuclear, mitochondrial, chloroplast or viral)
--mfreq STR,...
List of state frequencies
--mrate STR,...
List of rate heterogeneity among sites (e.g. -mrate E,I,G,I+G,R is used for -m MF)
--cmin NUM
Min categories for FreeRate model [+R] (default: 2)
--cmax NUM
Max categories for FreeRate model [+R] (default: 10)
--merit AIC|AICc|BIC
Akaike|Bayesian information criterion (default: BIC)
--mtree
Perform full tree search for every model
--madd STR,...
List of mixture models to consider
--mdef FILE
Model definition NEXUS file (see Manual)
--modelomatic
Find best codon/protein/DNA models (Whelan et al. 2015)
PARTITION-FINDER:
--merge
Merge partitions to increase model fit
--merge greedy|rcluster|rclusterf
Set merging algorithm (default: rclusterf)
--merge-model 1|all
Use only 1 or all models for merging (default: 1)
--merge-model STR,...
Comma-separated model list for merging
--merge-rate 1|all
Use only 1 or all rate heterogeneity (default: 1)
--merge-rate STR,...
Comma-separated rate list for merging
--rcluster NUM
Percentage of partition pairs for rcluster algorithm
--rclusterf NUM
Percentage of partition pairs for rclusterf algorithm
--rcluster-max NUM
Max number of partition pairs (default: 10*partitions)
SUBSTITUTION MODEL:
-m STRING
Model name string (e.g. GTR+F+I+G)
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,
FLAVI,
Q.LG, Q.pfam, Q.pfam_gb, Q.bird, Q.mammal, Q.insect, Q.plant, Q.yeast
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:
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)
Non-reversible:
STRSYM (strand symmetric model, equiv. WS6.6), NONREV, UNREST (unrestricted model,
equiv. 12.12)
Otherwise:
Name of file containing user-model parameters
STATE FREQUENCY:
-m ...+F
Empirically counted frequencies from alignment
-m ...+FO
Optimized frequencies by maximum-likelihood
-m ...+FQ
Equal frequencies
-m ...+FRY
For DNA, freq(A+G)=1/2=freq(C+T)
-m ...+FWS
For DNA, freq(A+T)=1/2=freq(C+G)
-m ...+FMK
For DNA, freq(A+C)=1/2=freq(G+T)
-m ...+Fabcd
4-digit constraint on ACGT frequency (e.g. +F1221 means f_A=f_T, f_C=f_G)
-m ...+FU
Amino-acid frequencies given protein matrix
-m ...+F1x4
Equal NT frequencies over three codon positions
-m ...+F3x4
Unequal NT frequencies over three codon positions
RATE HETEROGENEITY AMONG SITES:
-m ...+I
A proportion of invariable sites
-m ...+G[n]
Discrete Gamma model with n categories (default n=4)
-m ...*G[n]
Discrete Gamma model with unlinked model parameters
-m ...+I+G[n]
Invariable sites plus Gamma model with n categories
-m ...+R[n]
FreeRate model with n categories (default n=4)
-m ...*R[n]
FreeRate model with unlinked model parameters
-m ...+I+R[n]
Invariable sites plus FreeRate model with n categories
-m ...+Hn
Heterotachy model with n classes
-m ...*Hn
Heterotachy model with n classes and unlinked parameters
--alpha-min NUM
Min Gamma shape parameter for site rates (default: 0.02)
--gamma-median
Median approximation for +G site rates (default: mean)
--rate Write empirical Bayesian site rates to .rate file
--mlrate
Write maximum likelihood site rates to .mlrate file
POLYMORPHISM AWARE MODELS (PoMo):
-s FILE
Input counts file (see manual)
-m ...+P
DNA substitution model (see above) used with PoMo
-m ...+N<POPSIZE>
Virtual population size (default: 9)
-m ...+WB|WH|S]
Weighted binomial sampling
-m ...+WH
Weighted hypergeometric sampling
-m ...+S
Sampled sampling
-m ...+G[n]
Discrete Gamma rate with n categories (default n=4)
COMPLEX MODELS:
-m "MIX{m1,...,mK}"
Mixture model with K components
-m "FMIX{f1,...fK}"
Frequency mixture model with K components
--mix-opt
Optimize mixture weights (default: detect)
-m ...+ASC
Ascertainment bias correction
--tree-freq FILE
Input tree to infer site frequency model
--site-freq FILE
Input site frequency model file
--freq-max
Posterior maximum instead of mean approximation
TREE TOPOLOGY TEST:
--trees FILE
Set of trees to evaluate log-likelihoods
--test NUM
Replicates for topology test
--test-weight
Perform weighted KH and SH tests
--test-au
Approximately unbiased (AU) test (Shimodaira 2002)
--sitelh
Write site log-likelihoods to .sitelh file
ANCESTRAL STATE RECONSTRUCTION:
--ancestral
Ancestral state reconstruction by empirical Bayes
--asr-min NUM
Min probability of ancestral state (default: equil freq)
TEST OF SYMMETRY:
--symtest
Perform three tests of symmetry
--symtest-only
Do --symtest then exist
--symtest-remove-bad
Do --symtest and remove bad partitions
--symtest-remove-good
Do --symtest and remove good partitions
--symtest-type MAR|INT
Use MARginal/INTernal test when removing partitions
--symtest-pval NUMER
P-value cutoff (default: 0.05)
--symtest-keep-zero
Keep NAs in the tests
CONCORDANCE FACTOR ANALYSIS:
-t FILE
Reference tree to assign concordance factor
--gcf FILE
Set of source trees for gene concordance factor (gCF)
--df-tree
Write discordant trees associated with gDF1
--scf NUM
Number of quartets for site concordance factor (sCF)
-s FILE
Sequence alignment for --scf
-p FILE|DIR
Partition file or directory for --scf
--cf-verbose
Write CF per tree/locus to cf.stat_tree/_loci
--cf-quartet
Write sCF for all resampled quartets to .cf.quartet