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

FlowerPower is a 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