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.