Background

DupliPHY and DupliPHY-ML¹ are command line tools to determine the evolutionary history of gene families using weighted parsimony² and maximum likelihood³. The tools accept a newick string species phylogeny and a list of gene family sizes. DuipliPHY allows the user to also provide a weight matrix specifying the costs of gene gain and loss, while DupliPHY-ML allows the user to select between two different models of gene gain and loss.
The tools will output the ancestral family sizes for each gene family in a tab delimited format. The tool can be applied to single gene families or run for whole genomic studies.

DupliPHY and DupliPHY-ML are available as executable jar files and should run on any operating system.

The source code is available for DupliPHY. The source code for DupliPHY-ML is available on request.

Download

Right click here and choose "Save Link As" to download the DupliPHY executable jar file complete with user guide and example data sets.

Right click here and choose "Save Link As" to download the DupliPHY source code.

Right click here and choose "Save Link As" to download the DupliPHY-ML executable jar file complete with user guide and example data sets.

Data

All downloads contain example data. This is a subset of the Drosophila dataset from the publication. The full Drosophila data set can be downloaded here.

References

1. Ames RM, Money D, Ghatge V, Whelan S and Lovell SC.
Determining the evolutionary history of gene families.
In Preparation.

2. Sankoff D.
Minimal mutation trees of sequences.
SIAM Journal of Applied Mathematics 1975, 28:35.

3. Felsenstein J.
Inferring phylogenies.
Sinauer Associates. 2004.