Wikiomics:Orthologues

=Protein orthologues=

For simple orthologue retrieval in vertebrates use Ensembl. Each gene has there a list of best reciprocal hits in other species.

Review paper: PLOS One 2007

For clustering multiple sequences:


 * Inparanoid
 * OrthoMCL TribeMCL
 * CD-HIT fast clustering of proteins and i.e. ESTs.
 * FlowerPower protein homology clustering algorithm, similar to PSI-BLAST in its iterated approach to alignment, profile construction, and homolog identification, but with distinct differences.


 * Exonerate tool from sanger

Orthologues retrival

 * OrthoMCL

=Other=


 * Metazome organizes the proteomes of twenty-four metazoans into gene families defined at nine ancestral nodes on the metazoan evolutionary tree. Shows synthenty.

=References=
 * 1) “Joining forces in the quest for orthologs.” Text, 2009. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768974/.
 * 2) “Large-scale assignment of orthology: back to phylogenetics?.” Text, 2008. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760865/?tool=pubmed.
 * 3) “PLoS ONE: Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes.” http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0000383.