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:
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