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Programs used: MAFFT, ClipKIT, IQTREE2, PhyKIT, & OrthoSNAP
Datasets of organisms with complex evolutionary histories, especially complex patterns of duplications and loss, can have few single-copy orthologs. As a result, it may be helpful to use newer strategies to obtain single-copy orthologs that are nested in larger, multi-copy orthogroups (OGs). To do so, we will implement a splitting and pruning procedure in OrthoSNAP. This software breaks or “snaps” branches in multi-copy gene families to identify single-copy OGs nested within; thus, single-copy OGs identified by OrthoSNAP are termed SNAP-OGs.
This figure describes how OrthoSNAP works and what it takes as input.