InParanoid

From BioPerl

InParanoid

Eukaryotic Orthologous Groups based on best reciprocal hits with correction for paralogous families and a bootstrapping approach [1]. A precomputed database [2] is available for a set of eukaryotic genomes.

MultiParanoid

Combine multiple in-paranoid pairwise orthology analyses into a single set of orthologous gene predictions. Multiparanoid[3] site describes the approach in more detail.

References

1. Remm M, Storm CE, and Sonnhammer EL. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 2001 Dec 14; 314(5) 1041-52. doi:10.1006/jmbi.2000.5197 pmid:11743721. PubMed HubMed [remm2001]
2. O'Brien KP, Remm M, and Sonnhammer EL. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 2005 Jan 1; 33(Database issue) D476-80. doi:10.1093/nar/gki107 pmid:15608241. PubMed HubMed [obrien2005]
3. Alexeyenko A, Tamas I, Liu G, and Sonnhammer EL. Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 2006 Jul 15; 22(14) e9-15. doi:10.1093/bioinformatics/btl213 pmid:16873526. PubMed HubMed [multiparanoid]

All Medline abstracts: PubMed HubMed