InParanoid

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 |
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 |
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 |