Gene Family Construction and Ortholog Determination in Phytozome

Phytozome (http://www.phytozome.net) is a comparative hub for plant genome data and analysis. As a key feature of Phytozome 10, we provide a set of automatically generated protein-coding gene families along with corresponding phylogenetic trees, profiles, and ortholog and paralog assignments. Here, we describe our family construction pipeline and ortholog and paralog calling procedures. We compare our ortholog assignments to a synteny-based “gold standard” set as well as those determined by previously published methods, including Inparanoid and the EnsemblCompara pipeline. Finally, we present search, visualization, and assignment tools available at Phytozome for working with plant gene families and homology data.