jmodeltest - HPC selection of models of nucleotide substitution

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

jmodeltest 2.1.10                                  August 2016                                     JMODELTEST(1)

       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.

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

       jmodeltest - HPC selection of models of nucleotide substitution

-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)

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]