Note, steps within objectives that have fill-in-the-blank prompts are indicated as such using blue color font. Please fill in these prompts. Additionally, if the software you are trying to use isn’t in your path, it is likely in ~/software.

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.