PROTEIN = .faa
    PROTEIN_ALIGN = [ .faa.mafft Mafft ]
    BLASTP = .blastp
    FNAFILE = .fna
    BOUNDEDFILE = .fba
    TREE = .treefix.tree.DN.branlen

Contains The prefix and file-type suffices for each of the files used in the compara analysis. For each orthogroup, there should be a single folder containing one file of each type for loading into the compara database.

The alignment method used for aligned protein files should also be specified (e.g. PROTEIN_ALIGN = [ .faa.mafft Mafft ].