DupliPHY and DupliPHY-ML1 are tools to determine the evolutionary history of gene families using weighted parsimony or maximum likelihood. DupliPHY and DupliPHY-ML are implemented in Java and available as executable jar files, bundled with the source code and an example data set. The tool should run on any operating system.
Ames RM, Money D, Ghatge VP, Whelan S and Lovell SC.
Determining the evolutionary history of gene families.
Bioinformatics (2012) 28(1): 48-55.