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Salvatore Cosentino / sonicparanoid2
GNU General Public License v3.0 onlySonicParanoid is a stand-alone software tool for the identification of orthologous relationships among multiple species.
For details go to the wiki-page
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PHD / proteinortho
GNU General Public License v3.0 or laterProteinortho is a tool to detect orthologous genes within different species. (Download)
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Felix Thalén / phylopypruner
GNU General Public License v3.0 or laterA tree-based orthology inference program with additional functionality for reducing contamination.
Updated