Table 1.

Phamerator Features and Modifications

Feature	Updates provided in new version	Justification
Biopython compatibility	Works with BioPython 1.64	Continued compatibility with future Biopython versions
Building the Phamerator database	Added prompts for username, password, server location, and database name at each step	The new prompts replace what was once written directly into the code
ClustalO alignments	ClustalO may be used instead of ClustalW to perform alignments	ClustalO is newer and is faster
Computation progress	Fixed script displaying the progress of BLAST and ClustalW	Helps users estimate when these jobs will finish
Pham and cluster tables	Column listing conserved domains for each pham was added to these tables	Used to quickly determine putative functions of proteins in a pham
Domain and pham labels in genome maps	Added whitespace to the right of these maps	Labels near the end of these maps are now visible
Delete BLAST and ClustalW scores	Users are prompted to delete or keep all scores when adding or removing phages	Scores can be deleted following major modifications to the database

This table describes features of Phamerator, the updates provided by the new version we provide, and the justification of why these modifications were necessary