Skip to main content

Table 1 Phamerator Features and Modifications

From: Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies

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