For assigning Stentor gene models into ortholog groups
This repository contains a script for categorizing Stentor OrthoMCL results and organizing into a table, as well as text files containing lists of ortholog groups with specific phyletic patterns. Resulting data can be found in Figure 2B, Figure S2A-B, and Table S2 of the Stentor genome paper.
Basic description of workflow:
- OrthoMCL was run on the Stentor predicted proteins to organize them into ortholog groups
- Lists of ortholog groups that comprised specific phyletic patterns were created
- When a sequence didn't match any OrthoMCL group, orthologs were looked for in other ciliate proteomes
- When a sequence didn't match any ortholog group, including in other ciliate proteomes, Stentor paralogs were looked for
- A table was generated containing each Stentor gene, what ortholog group it belongs to (if any), and the group's phyletic pattern