The first step is to familiarize yourself with the key concepts and literature. Here is a list of review papers and book chapters to get you started.

• Orthologs, Paralogs, and Evolutionary Genomics. Paper.
• Orthology: Promises and Challenges. Paper.

Watch YouTube videos: “Introduction to molecular evolution & phylogenetics”: Link starting at 1:28:00.

Next, we need to familiarize ourselves with the literature. These are the latest methods papers:

• Orthology inference at scale with FastOMA. Paper.
• OrthoFinder: phylogenetic orthology inference for comparative genomics. Paper.
• SonicParanoid: fast, accurate and easy orthology inference Paper.

Then, the goal is to identify the knowledge gaps and areas for improvement. An important step is to run the tools on small datasets and check their outputs.