ComPhy (Genome Composite Distance Phylogeny) is a java based tool for whole-genome gene set phylogeney inferences.The software determines a prokaryotic phylogeny by calculating a composite distance based on the comparison of complete gene sets between two genomes. It does not require multiple sequence alignment and is fully automated. The composite distance between two genomes is defined by three components: Gene Dispersion Distance (GDD), Gene Content Distance (GCD), and Genome Breakpoint-based Distance (GBD). GDD quantifies the dispersion of ortholog clusters along the genomic coordinates from one genome to another; GCD measures the level of shared orthologs between two genomes; GBD measures the shared break-points between two genomes. The phylogenetic tree is constructed using a neighbour joining method using Phylip from the distance matrix calculated by the composite distance. ComPhy also provides the performance measure of the generated tree against Bergey’s taxonomy system.
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BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S5.
ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets.
Lin GN, Cai Z, Lin G, Chakraborty S, Xu D.