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M ulti P aranoid
A database of multi-species clusters of orthologs
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Interactive WWW access to MultiParanoid

You can download the MultiParanoid program and use it locally.

Using the program, please cite the article
Andrey Alexeyenko, Ivica Tamas, Gang Liu, and Erik L.L. Sonnhammer (2006) Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22: e9-e15.
[Abstract] [PDF]

Supplementary files to the paper are now located here: