Clan_Check analyses single-copy phylogenetic trees to assess if they violate clans defined by the user. This is designed for large-scale phylogenomic analyses where the user may have thousands of phylogenetic trees. This tool can help enrich the data for orthologs, by identifying where paralogy has caused violation of “well known” clans in outgroups.
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Siu-Ting, Karen, et al.
Inadvertent paralog inclusion drives artefactual topologies and timetree estimates in phylogenomics.
Molecular biology and evolution (2019).