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:
- 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
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.