Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood.

Abstract

Count is a software package for the analysis of numerical profiles on a phylogeny. It is primarily designed to deal with profiles derived from the phyletic distribution of homologous gene families, but is suited to study any other integer-valued evolutionary characters. Count performs ancestral reconstruction, and infers family- and lineage-specific characteristics along the evolutionary tree. It implements popular methods employed in gene content analysis such as Dollo and Wagner parsimony, propensity for gene loss, as well as probabilistic methods involving a phylogenetic birth-and-death model. Count is available as a stand-alone Java application, as well as an application bundle for MacOS X, at the web site http://www.iro.umontreal.ca/ approximately csuros/gene_content/count.html. It can also be launched using Java Webstart from the same site. The software is distributed under a BSD-style license. Source code is available upon request from the author.