init_orthofinder

This script collects the protein FASTAs in folder_structure/OrthoFinder/fastas and prints the command to run OrthoFinder.

Usage

export FOLDER_STRUCTURE=/path/to/folder_structure
init_orthofinder --representatives_only

Result

The script creates the following structure:

folder_structure
├── ...
└── OrthoFinder
    └── fastas
        ├── GENOME1.faa
        ├── GENOME2.faa
        └── ...

Parameters

• --representatives_only: Only include representative genomes (optional)

Next Steps

After running this command, you'll need to:

1. Run the OrthoFinder command that is printed
2. Use import_orthofinder to process the results

Help

init_orthofinder --help