Revert "took out disambiguating column names in combine_files, updated POD."
Revert "took out disambiguating column names in combine_files, updated POD."

This reverts commit 9404cb594d5b9819993a7f063d667e2abe0fb5e3.

TheMolecularEcologist/phylogenomics,TheMolecularEcologist/phylogenomics,daisieh/phylogenomics,daisieh/phylogenomics,daisieh/phylogenomics,TheMolecularEcologist/phylogenomics