orthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

Molecular evolution studies, such as phylogenomic studies and genome-wide surveys of positive selection, often rely on gene families of single-copy orthologs (SC-OGs). In contrast, large gene families with multiple homologs in one 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. From 46,645 orthologous groups of genes inferred using graph-based clustering of sequence similarity scores across four separate eukaryotic datasets, we identified 6,634 SC-OGs; using orthoSNAP on the remaining 40,011 orthologous groups of genes, we identified an additional 6,630 SNAP-OGs. Comparison of SNAP-OGs and SC-OGs revealed that their phylogenetic information content was similar. orthoSNAP is useful for increasing the number of markers used in molecular evolution data matrices, a critical step for robustly inferring and exploring the tree of life.