POPE provides an integrated platform for automatic ortholog identification. Intermediate steps can be visualized, modified and analyzed in order to assess and improve the underlying quality of orthology and paralogy assignments.
POPE (Phylogeny, Ortholog and Paralog Extractor) is a Java and Perl program, developed in order to aid in phylogenetic data analysis using a large number of proteins. POPE includes routines to sort phylogenetic trees based on the presence or absence of orthologs of the target gene, at the same time as graphically displaying alignments, phylogenies and domain locations within the multiple alignments.
Perl, BioPerl Java 1.5 or higher
List of external programs used by Pope:
Reference