yangzy2019 / modelomatic

Modelomatic - A software for model selection across state-spaces

#Modelomatic

Written by Simon Whelan, with contributions from James Allen, Ben Blackburne and David Talavera

ModelOMatic is a C++ program designed for rapid phylogenetic model selection on protein coding genes. Please see the manual for details of the program and its settings.

ModelOMatic is distributed free of charge for personal and academic use only under a GNU GPL v3. Modelomatic is a piece of academically developed software and should be used at your own risk!

Pay attention to the output and use your own judgements when performing analysis. Modelomatic uses lots of heuristics that seem to perform well when tested across the PANDIT database, but they may not perform well on your data.

##Download information

• Precompiled binaries are available here
• The user manual is available here
• Example files are available here

##Version history Modelomatic will be periodically updated and changes that may affect the outcome of your analyses will be announced here. Minor fixes that address bugs that are not expected to change results are not included here.

• v1.03 -> v1.04 (5Aug16): There was a critical error where likelihoods from large families were not computed correctly (usually for codon models). The symptoms of this bug are lots of weird short branches and unreasonably high likelihoods.

##Models tested in Modelomatic

• RY
• DNA
  • JC
  • FEL
  • K2P
  • HKY
  • REV
• AA
  • EQU
  • BLOSUM62
  • DAY
  • JTT
  • WAG
  • LG
  • VT
  • cpREV
  • mtArt
  • mtMam
  • mtREV
  • rtREV
  • HIVb
  • HIVw
• Codon
  • F0
  • F1X4
  • F3X4
  • F64

##How to specify models with a configuration file

Modelomatic will look for configuration files $HOME/.modelomatic.ini and $PWD/modelomatic.ini. Configurations in the second file will be laid over the first (i.e. models turned off in $HOME/.modelomatic.ini can be switched back on in $PWD/modelomatic.ini). The format is standard INI, and models are specified with 0/1, as below:

[Amino Acid]
;Ignore Viral models
rtREV=0
HIVb=0
HIVw=0

[Codon]
F0=0

Currently only Amino Acid and Codon models can be specified. The default case is to run everything. The INI file is case insensitive.