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