Step 2 - gene age class assignment

Given mandatory OrthoFinder results files as described here gene age classes can be extracted with oggmap or pre-calculated orthomaps can be imported.

How to extract an orthomap (gene age class) from OrthoFinder results

Please download the notebooks from here or please click below to view the content.

• oggmap: Step 2 - gene age class assignment
  • Notebook file
  • Import libraries
  • Import oggmap python package submodules
  • Use OrthoFinder results to get gene age classification
  • Ensembl release-105
  • Ensembl release-110
    • Gene age assignments per query species lineage node
    • Visualize number of species along query lineage and counts per gene age class
  • Use pre-calculated gene age classification
    • Gene age assignments per query species lineage node