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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.

Orthologues retrival


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


  1. “Joining forces in the quest for orthologs.” Text, 2009.
  2. “Large-scale assignment of orthology: back to phylogenetics?.” Text, 2008.
  3. “PLoS ONE: Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes.”