Intro
Count is a software package for the evolutionary analysis of homolog family sizes (phylogenetic profiles), or other numerical census-type characters along a phylogeny. The principal data consist of the distribution of homolog family sizes across multiple genomes: for each (gene) family, that table gives the number of homologs identified in each genome. Count has been tested using data from the arCOG and KOG databases. The implemented tasks include the following.
- Family filtering by family size, presence in selected genomes, or other criteria.
- Parameter optimization for a phylogenetic birth-and-death model.
- Ancestral reconstruction by Dollo parsimony.
- Ancestral reconstruction by symmetric or asymmetric Wagner parsimony.
- Ancestral reconstruction by posterior probabilities in a phylogenetic birth-and-death model.
Current version
Count is written entirely in Java, and, thus, can be used in different operating systems, including Mac OS X, Microsoft Windows, and various Unix/Linux versions. The software is packaged in a JAR file, and can be executed in Java versions 1.13 and above, on a 64-bit Java VM.
Please download the current version from github at https://github.com/csurosm/count.
Old versions
Downloadable files
- count-usage.pdf: User's Guide
- Count.jar: JAR package
- Count.dmg: MacOS disk image
- Count.zip: Microsoft Windows package
- Count.tgz: Unix/Linux package
- test.tar.gz: test data