ModelGenerator is a free software program designed and written by Thomas Keane.

ModelGenerator is a model selection program that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models.

ModelGenerator has been written using the Java programming language, and will run on any operating system supporting the Java VM.

ModelGenerator accepts both Fasta and Phylip format alignments. ModelGenerator uses the PAL library to perform its calculations

If you wish to receive the source code or have problems running ModelGenerator - email me: thomaskeane_at_gmail.com

Download

Startup command

java -jar modelgenerator.jar alignment_file num_gamma_categories

If you get a java.lang.OutOfMemory error then increase the amount of memory available to java using the -Xmx option (e.g. java -Xmx200m ....)

Online Execution

ModelGenerator is now available for online execution from here. You can upload your alignments and the results are emailed back to you.

Citation: Thomas M Keane, Christopher J Creevey , Melissa M Pentony, Thomas J Naughton and James O McInerney (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified, BMC Evolutionary Biology, 6:29