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 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 Paper
• SonicParanoid 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.