zol

• Update/Fix: Added a new option -pfp for controlling annotation of Pfam domains in zol. The default annotation of Pfam domains has also changed. By default, Pfam domains are now annotated along consensus sequences of ortholog groups at the domain-resolution using gathering thresholds. Domain-resolution reporting/filtering was used for zol's -dom mode previously but not for the annotation of ortholog group consensus sequences which reported hits at the protein-resolution (which can lead to slight differences in annotation reporting/filtering). Reports of matches to other HMM-based databases referenced by zol for functional annotation are still provided at the protein-resolution. This is because the profile-HMMs for those largely correspond to full proteins rather than individual domains like for the Pfam database. Note, regardless of whether Full (protein-resolution) annotation of Pfam is requested or not, domain-resolution annotation of Pfam domains will be used for chopping-up proteins if -dom mode is requested.
• Update/Fix: Updated annotation of IS-elements/transposons to no longer include proteins labeled as ~~~Passenger Gene~~~ in the ISfinder database. Added a note in the SALT resulting spreadsheet that proteins labeled as "Accessory Gene" are still included in the database which could impact interpretation of support for lateral/horizontal transfer.

Full Changelog: https://github.com/Kalan-Lab/zol/compare/v1.6.15...v1.6.16