OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees.

ABSTRACT: Molecular evolution studies, such as phylogenomic studies and genome-wide surveys of selection, often rely on gene families of single-copy orthologs (SC-OGs). Large gene families with multiple homologs in 1 or more species-a phenomenon observed among several important families of genes such as transporters and transcription factors-are often ignored because identifying and retrieving SC-OGs nested within them is challenging. To address this issue and increase the number of markers used in molecular evolution studies, we developed OrthoSNAP, a software that uses a phylogenetic framework to simultaneously split gene families into SC-OGs and prune species-specific inparalogs. We term SC-OGs identified by OrthoSNAP as SNAP-OGs because they are identified using a splitting and pruning procedure

SUBMITTER: Steenwyk JL 

PROVIDER: S-EPMC9595520 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature