Provided by: iqtree_2.0.7+dfsg-1_amd64 bug

NAME

       iqtree2 - efficient phylogenetic software by maximum likelihood

SYNOPSIS

       iqtree [-s ALIGNMENT] [-p PARTITION] [-m MODEL] [-t TREE] ...

DESCRIPTION

       IQ-TREE  multicore version 2.0.7 for Linux 64-bit built Jan 21 2022 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