Provided by: iqtree_1.6.9+dfsg-1_amd64 bug

NAME

       iqtree-mpi  -  efficient  phylogenetic  software  by  maximum  likelihood  (multiprocessor
       version)

SYNOPSIS

       iqtree-mpi -s <alignment> [OPTIONS]

DESCRIPTION

       --------------------------------------------------------------------------  [[43413,1],0]:
       A  high-performance  Open  MPI  point-to-point  messaging  module  was  unable to find any
       relevant network interfaces:

       Module: OpenFabrics (openib)

              Host: lgw01-amd64-023

       Another transport will be used instead, although this may result in lower performance.

       NOTE:   You   can   disable    this    warning    by    setting    the    MCA    parameter
       btl_base_warn_component_unused                            to                            0.
       --------------------------------------------------------------------------   IQ-TREE   MPI
       multicore  version  1.6.9  for Linux 64-bit built Jan  2 2019 Developed by Bui Quang Minh,
       Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

   GENERAL OPTIONS:
       -? or -h
              Print this help dialog

       -version
              Display version number

       -s <alignment>
              Input alignment in PHYLIP/FASTA/NEXUS/CLUSTAL/MSF format

       -st <data_type>
              BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect)

       -q <partition_file>
              Edge-linked partition model (file in NEXUS/RAxML format)

       -spp <partition_file> Like -q option but allowing partition-specific rates

       -sp <partition_file> Edge-unlinked partition model (like -M option of RAxML)

       -t <start_tree_file> or -t BIONJ or -t RANDOM
              Starting tree (default: 99 parsimony tree and BIONJ)

       -te <user_tree_file> Like -t but fixing user tree (no tree search performed)

       -o <outgroup_taxon>
              Outgroup taxon name for writing .treefile

       -pre <PREFIX>
              Prefix for all output files (default: aln/partition)

       -nt <num_threads>
              Number of cores/threads or AUTO for automatic detection

       -ntmax <max_threads> Max number of threads by -nt AUTO (default: #CPU cores)

       -seed <number>
              Random seed number, normally used for debugging purpose

       -v, -vv, -vvv
              Verbose mode, printing more messages to screen

       -quiet Quiet mode, suppress printing to screen (stdout)

       -keep-ident
              Keep identical sequences (default: remove & finally add)

       -safe  Safe likelihood kernel to avoid numerical underflow

       -mem RAM
              Maximal RAM usage for memory saving mode

       --runs NUMBER
              Number of indepedent runs (default: 1)

   CHECKPOINTING TO RESUME STOPPED RUN:
       -redo  Redo analysis even for successful runs (default: resume)

       -cptime <seconds>
              Minimum checkpoint time interval (default: 60 sec)

   LIKELIHOOD MAPPING ANALYSIS:
       -lmap <#quartets>
              Number of quartets for likelihood mapping analysis

       -lmclust <clustfile> NEXUS file containing clusters for likelihood mapping

       -wql   Print quartet log-likelihoods to .quartetlh file

   NEW STOCHASTIC TREE SEARCH ALGORITHM:
       -ninit <number>
              Number of initial parsimony trees (default: 100)

       -ntop <number>
              Number of top initial trees (default: 20)

       -nbest <number>
              Number of best trees retained during search (defaut: 5)

       -n <#iterations>
              Fix number of iterations to stop (default: auto)

       -nstop <number>
              Number of unsuccessful iterations to stop (default: 100)

       -pers <proportion>
              Perturbation strength for randomized NNI (default: 0.5)

       -sprrad <number>
              Radius for parsimony SPR search (default: 6)

       -allnni
              Perform more thorough NNI search (default: off)

       -g <constraint_tree> (Multifurcating) topological constraint tree file

       -fast  Fast search to resemble FastTree

   ULTRAFAST BOOTSTRAP:
       -bb <#replicates>
              Ultrafast bootstrap (>=1000)

       -bsam GENE|GENESITE
              Resample GENE or GENE+SITE for partition (default: SITE)

       -wbt   Write bootstrap trees to .ufboot file (default: none)

       -wbtl  Like -wbt but also writing branch lengths

       -nm <#iterations>
              Maximum number of iterations (default: 1000)

       -nstep <#iterations> #Iterations for UFBoot stopping rule (default: 100)

       -bcor <min_corr>
              Minimum correlation coefficient (default: 0.99)

       -beps <epsilon>
              RELL epsilon to break tie (default: 0.5)

       -bnni  Optimize UFBoot trees by NNI on bootstrap alignment

       -j <jackknife>
              Proportion of sites for jackknife (default: NONE)

   STANDARD NON-PARAMETRIC BOOTSTRAP:
       -b <#replicates>
              Bootstrap + ML tree + consensus tree (>=100)

       -bc <#replicates>
              Bootstrap + consensus tree

       -bo <#replicates>
              Bootstrap only

   SINGLE BRANCH TEST:
       -alrt <#replicates>
              SH-like approximate likelihood ratio test (SH-aLRT)

       -alrt 0
              Parametric aLRT test (Anisimova and Gascuel 2006)

       -abayes
              approximate Bayes test (Anisimova et al. 2011)

       -lbp <#replicates>
              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 TESTMERGEONLY
              Find best partition scheme (like PartitionFinder)

       -m TESTMERGE
              Find best partition scheme followed by tree inference

       -m MF+MERGE
              Find best partition scheme incl. FreeRate heterogeneity

       -m MFP+MERGE
              Like -m MF+MERGE followed by tree inference

       -rcluster <percent>
              Percentage of partition pairs (relaxed clustering alg.)

       -rclusterf <perc.>
              Percentage of partition pairs (fast relaxed clustering)

       -rcluster-max <num>
              Max number of partition pairs (default: 10*#partitions)

       -mset program
              Restrict search to models supported by other programs (raxml, phyml or mrbayes)

       -mset <lm-subset>
              Restrict search to a subset of the Lie-Markov models  Options  for  lm-subset  are:
              liemarkov, liemarkovry, liemarkovws, liemarkovmk, strandsymmetric

       -mset m1,...,mk
              Restrict search to models in a comma-separated list (e.g. -mset WAG,LG,JTT)

       -msub source
              Restrict  search  to  AA  models  for  specific  sources  (nuclear,  mitochondrial,
              chloroplast or viral)

       -mfreq f1,...,fk
              Restrict search to using a list of state  frequencies  (default  AA:  -mfreq  FU,F;
              codon: -mfreq ,F1x4,F3x4,F)

       -mrate r1,...,rk
              Restrict  search  to a list of rate-across-sites models (e.g. -mrate E,I,G,I+G,R is
              used for -m MF)

       -cmin <kmin>
              Min #categories for FreeRate model [+R] (default: 2)

       -cmax <kmax>
              Max #categories for FreeRate model [+R] (default: 10)

       -merit AIC|AICc|BIC
              Optimality criterion to use (default: all)

       -mtree Perform full tree search for each model considered

       -mredo Ignore model results computed earlier (default: reuse)

       -madd mx1,...,mxk
              List of mixture models to also consider

       -mdef <nexus_file>
              A model definition NEXUS file (see Manual)

   SUBSTITUTION MODEL:
       -m <model_name>

       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

              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: One  of  the  following,
              optionally prefixed by RY, WS or MK:

       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

              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.

              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 -optfromgiven option supplied)

              Otherwise: Name of file containing user-model parameters

              (rate parameters and state frequencies)

   STATE FREQUENCY:
              Append    one    of    the    following    +F...    to    -m    <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),

              +FWS is freq(A+T)=1/2=freq(C+G), +FMK is freq(A+C)=1/2=freq(G+T).

       +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).

       +FU    Amino-acid frequencies by the given protein matrix

       +F1x4 (codon model)
              Equal NT frequencies over three codon positions

       +F3x4 (codon model)
              Unequal NT frequencies over three codon positions

   MIXTURE MODEL:
       -m "MIX{model1,...,modelK}"
              Mixture model with K components

       -m "FMIX{freq1,...freqK}"
              Frequency mixture model with K components

       -mwopt Turn on optimizing mixture weights (default: none)

   RATE HETEROGENEITY AMONG SITES:
       -m modelname+I
              A proportion of invariable sites

       -m modelname+G[n]
              Discrete Gamma model with n categories (default n=4)

       -m modelname*G[n]
              Discrete Gamma model with unlinked model parameters

       -m modelname+I+G[n]
              Invariable sites plus Gamma model with n categories

       -m modelname+R[n]
              FreeRate model with n categories (default n=4)

       -m modelname*R[n]
              FreeRate model with unlinked model parameters

       -m modelname+I+R[n]
              Invariable sites plus FreeRate model with n categories

       -m modelname+Hn
              Heterotachy model with n classes

       -m modelname*Hn
              Heterotachy model with n classes and unlinked parameters

       -a <Gamma_shape>
              Gamma shape parameter for site rates (default: estimate)

       -amin <min_shape>
              Min Gamma shape parameter for site rates (default: 0.02)

       -gmedian
              Median approximation for +G site rates (default: mean)

       --opt-gamma-inv
              More thorough estimation for +I+G model parameters

       -i <p_invar>
              Proportion of invariable sites (default: estimate)

       -wsr   Write site rates to .rate file

       -mh    Computing  site-specific  rates  to  .mhrate file using Meyer & von Haeseler (2003)
              method

   POLYMORPHISM AWARE MODELS (PoMo):
       -s <counts_file>
              Input counts file (see manual)

       -m <MODEL>+P
              DNA substitution model (see above) used with PoMo

       +N<POPSIZE>
              Virtual population size (default: 9)

       +[WB|WH|S]
              Sampling method (default: +WB), WB: Weighted binomial, WH: Weighted  hypergeometric
              S: Sampled sampling

       +G[n]  Discrete Gamma rate model with n categories (default n=4)

   ASCERTAINMENT BIAS CORRECTION:
       -m modelname+ASC
              Correction for absence of invariant sites in alignment

   SINGLE TOPOLOGY HETEROTACHY MODEL:
       -m <model_name>+H[k]
              Heterotachy model mixed branch lengths with k classes

       -m "MIX{m1,...mK}+H"

       -nni-eval <m>
              Loop m times for NNI evaluation (default m=1)

   SITE-SPECIFIC FREQUENCY MODEL:
       -ft <tree_file>
              Input tree to infer site frequency model

       -fs <in_freq_file>
              Input site frequency model file

       -fmax  Posterior maximum instead of mean approximation

   CONSENSUS RECONSTRUCTION:
       -t <tree_file>
              Set of input trees for consensus reconstruction

       -minsup <threshold>
              Min split support in range [0,1]; 0.5 for majority-rule consensus (default: 0, i.e.
              extended consensus)

       -bi <burnin>
              Discarding <burnin> trees at beginning of <treefile>

       -con   Computing consensus tree to .contree file

       -net   Computing consensus network to .nex file

       -sup <target_tree>
              Assigning support values for <target_tree> to .suptree

       -suptag <name>
              Node name (or ALL) to assign tree IDs where node occurs

   ROBINSON-FOULDS DISTANCE:
       -rf_all
              Computing all-to-all RF distances of trees in <treefile>

       -rf <treefile2>
              Computing all RF distances between two sets  of  trees  stored  in  <treefile>  and
              <treefile2>

       -rf_adj
              Computing RF distances of adjacent trees in <treefile>

   TREE TOPOLOGY TEST:
       -z <trees_file>
              Evaluating a set of user trees

       -zb <#replicates>
              Performing BP,KH,SH,ELW tests for trees passed via -z

       -zw    Also performing weighted-KH and weighted-SH tests

       -au    Also performing approximately unbiased (AU) test

   ANCESTRAL STATE RECONSTRUCTION:
       -asr   Ancestral state reconstruction by empirical Bayes

       -asr-min <prob>
              Min probability of ancestral state (default: equil freq)

   GENERATING RANDOM TREES:
       -r <num_taxa>
              Create a random tree under Yule-Harding model

       -ru <num_taxa>
              Create a random tree under Uniform model

       -rcat <num_taxa>
              Create a random caterpillar tree

       -rbal <num_taxa>
              Create a random balanced tree

       -rcsg <num_taxa>
              Create a random circular split network

       -rlen <min_len> <mean_len> <max_len>
              min, mean, and max branch lengths of random trees

   MISCELLANEOUS:
       -wt    Write locally optimal trees into .treels file

       -blfix Fix branch lengths of user tree passed via -te

       -blscale
              Scale branch lengths of user tree passed via -t

       -blmin Min branch length for optimization (default 0.000001)

       -blmax Max branch length for optimization (default 100)

       -wsr   Write site rates and categories to .rate file

       -wsl   Write site log-likelihoods to .sitelh file

       -wslr  Write site log-likelihoods per rate category

       -wslm  Write site log-likelihoods per mixture class

       -wslmr Write site log-likelihoods per mixture+rate class

       -wspr  Write site probabilities per rate category

       -wspm  Write site probabilities per mixture class

       -wspmr Write site probabilities per mixture+rate class

       -wpl   Write partition log-likelihoods to .partlh file

       -fconst f1,...,fN
              Add constant patterns into alignment (N=#nstates)

       -me <epsilon>
              LogL epsilon for parameter estimation (default 0.01)

       --no-outfiles
              Suppress printing output files

       --eigenlib
              Use Eigen3 library

       -alninfo
              Print alignment sites statistics to .alninfo

       -czb   Collapse zero branches in final tree

       --show-lh
              Compute tree likelihood without optimisation