phyloCOP – Greedy Phylogeny-Based Algorithm for Orthology Assignment
PhyloCOP (phylogeny-based Clusters of Orthologous Proteins) is a customizable program for the assignment of orthologous genes into clusters. PhyloCOP detects transitive orthologous relationships between highly diverse prokaryotic proteins and assigns them into orthologous clusters, simultaneously excluding paralogy. Orthology assignment is based on best BLAST (Basic Local Alignment Search Tool) protein sequence similarity hits between pairs of genomes.
PhyloCOP is implemented in Perl and executed from a command line. A previous installation of the CPAN (Comprehensive Perl Archive Network) Perl modules Getopt::Std, Scalar::Util and File::Spec::Functions might be required. A script for multiple pairwise protein BLAST runs “blastloop.pl” can be downloaded together with phyloCOP. The previous installation of BLAST (Basic Local Alignment Search Tool) is required.
- phyloCOP.zip PhyloCOP including manual and example files
- phyloCOP_manual.pdf PhyloCOP manual
PhyloCOP is a non-profit project. It is published under the GNU General Public License (GPL 3).
Contact: Sabine Thuß
