NAME

       jmodeltest - HPC selection of models of nucleotide substitution

SYNOPSIS

       jmodeltest   -d  sequenceFileName  [-getPhylip]  [-ckp  checkpointFileName.ckp]  [-n  executionName]  [-t
       fixed|BIONJ|ML] [-u userTreeFileName] [-o outputFileName] [-S NNI|SPR|BEST] [-AIC] [-AICc]  [-BIC]  [-DT]
       [-c  confidenceInterval]  [-s  3|5|7|11|203]  [-f]  [-i]  [-g  numberOfCategories]  [-uLNL]  [-dLRT]  [-h
       confidenceInterval] [-hLRT] [-O {ftvwxgp}] [-a] [-z] [-p] [-v] [-w] [-tr numberOfThreads]  [-machinesfile
       machinesFileName]

DESCRIPTION

       jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It
       implements five different model selection strategies: hierarchical and dynamical likelihood  ratio  tests
       (hLRT  and  dLRT),  Akaike  and Bayesian information criteria (AIC and BIC), and a decision theory method
       (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged
       parameter  estimates,  including  model-averaged tree topologies.  jModelTest 2 includes High Performance
       Computing (HPC) capabilities and additional features like new strategies for  tree  optimization,  model-
       averaged  phylogenetic trees (both topology and branch length), heuristic filtering and automatic logging
       of user activity.

OPTIONS

       -a

              estimate model-averaged phylogeny for each active criterion (e.g., -a) (default is false)

       -AIC

              calculate the Akaike Information Criterion (e.g., -AIC) (default is false)

       -AICc

              calculate the corrected Akaike Information Criterion (e.g., -AICc) (default is false)

       -BIC

              calculate the Bayesian Information Criterion (e.g., -BIC) (default is false)

       -DT

              calculate the decision theory criterion (e.g., -DT) (default is false)

       -c confidenceInterval

              confidence interval (e.g., -c 90) (default is 100)

       -ckp checkpointFileName

              Loads a checkpointing file

       -d sequenceFileName

              input data file (e.g., -d data.phy)

       -dLRT

              do dynamical likelihood ratio tests (e.g., -dLRT)(default is false)

       -f

              include models with unequals base frecuencies (e.g., -f) (default is false)

       -g numberOfCategories

              include models with rate variation among sites and number of categories (e.g., -g 8)  (default  is
              false & 4 categories)

       -G threshold

              heuristic search. Requires a threshold > 0 (e.g., -G 0.1)

       -getPhylip

              converts the input file into phylip format

       -h confidenceInterval

              confidence level for the hLRTs (e.g., -a0.002) (default is 0.01)

       -H informationCriterion

              information  criterion  for  clustering  search  (AIC,  AICc, BIC). (default is BIC) this argument
              applies only for 203 substitution schemes (e.g., -s 203 -H AIC)

       -help

              displays this help message

       -hLRT

              do hierarchical likelihood ratio  tests  (default  is  false)  hypothesis  testing  order  can  be
              specified with -O argument

       -i

              include models with a proportion invariable sites (e.g., -i) (default is false)

       -machinesfile manchinesFileName

              gets the processors per host from a machines file

       -n executionName

              execution name for appending to the log filenames (default: current time yyyyMMddhhmmss)

       -o outputFileName

              set output file (e.g., -o jmodeltest.out)

       -O hypothesisOrder

              hypothesis order for the hLRTs (e.g., -hLRT -O gpftv) (default is ftvwxgp)

              f=freq,  t=titvi,  v=2ti4tv(subst=3)/2ti(subst>3),  w=2tv, x=4tv, g=gamma, p=pinv this argument is
              used only if -hLRT argument is  set  'f','t','v','g','p'  are  mandatory  in  any  order.  'w'  is
              optional,  and  'x'  requires  'w'  to be present thus, length should be 5, 6 *including 'w') or 7
              (including both 'w' and 'x') e.g., -hLRT -O gpfvwxt

       -p

              calculate parameter importances (e.g., -p) (default is false)

       -r

              backward selection for the hLRT (e.g., -r) (default is forward)

       -s numberOfSubstitutionSchemes

              number of substitution schemes (e.g., -s 11) (it has to be 3,5,7,11,203; default is 3)

       --set-local-config localConfigurationFile

              set a local configuration file in replacement of conf/jmodeltest.conf

       --set-property propertyName=propertyValue

              set a new value for a property contained in the configuration file (conf/jmodeltest.conf)

       -S NNI|SPR|BEST

              tree topology search operation option (NNI (fast), SPR (a bit slower), BEST (best of NNI and SPR))
              (default is BEST)

       -t fixed|BIONJ|ML

              base tree for likelihood calculations (e.g., -t BIONJ)

              fixed  (common BIONJ-JC topology)

              BIONJ  (Neighbor-Joining topology)

              ML     (Maximum Likelihood topology) (default)

       -tr numberOfThreads

              number of threads to execute (default is 4)

       -u treeFileName

       user tree for likelihood calculations
              (e.g., -u data.tre)

       -uLnL

              calculate delta AIC,AICc,BIC against unconstrained likelihood (e.g., -uLnL)

              (default is false if the input alignment has gaps or ambiguous characters)

       -v

              do model averaging and parameter importances (e.g., -v) (default is false)

       -w

              write PAUP block (e.g., -w) (default is false)

       -z

              strict consensus type for model-averaged phylogeny (e.g., -z) (default is majority rule)

EXAMPLE

       jmodeltest -d sequenceFileName -i -f -g 4 -BIC -AIC -AICc -DT -v -a -w

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.