- This is the version used for the analyses in the initial version of the zol manuscript - however updates were made to the README, code comments, and help functions of arguments. Additionally: (i) a few lines were commented out and back in to ensure this is the version matching results in our study and (ii) because the directory structure of PGAP HMMs used for annotation changed recently - the script `setup_annotation_dbs.py` was updated to reflect the new structure.