OrthoGrafter: Rapid Identification of Orthologs from Precomputed Placement in Phylogenetic Trees

The identification of orthologs plays an important role in comparative genomics and function inference. Here, we present OrthoGrafter, a bioinformatics tool for taking one or more query sequences and inferring a set of orthologs drawn from the collection of 143 well annotated species in the PANTHER database of reconciled gene trees. OrthoGrafter takes sets of graft points output by the highly used TreeGrafter software (either the standalone package or InterProScan), and for each one, outputs a list of predicted orthologous genes from the grafted PANTHER tree (with the ability to additionally output paralog and xenolog sets). If the taxonomic identifier for the query is also provided, OrthoGrafter incorporates the novel step of adjusting the graft point to facilitate consistent taxonomic assignment for the graft within the reconciled gene family, which we demonstrate shows an improvement in the ortholog inference via correlation with orthologs provided by the OMA database. Lightweight and utilizing precomputed results to enable rapid determination of ortholog predictions for large sample groups, OrthoGrafter is available at https://github.com/pantherdb/OrthoGrafter. .