Phamerator

The BYU-modified Phamerator code is available here:  BYU Phamerator at GitHub and can be downloaded using git.
These programs run in the Linux Ubuntu operating system.

This PDF contains instructions:  BYU Phamerator Instructions.pdf
Instructions include how to:
  Set up a Ubuntu virtual machine
  Install the BYU-modified Phamerator and other software
  Use Phamerator to create and process a database of phage genomes
  Using the Phamerator user interface for phage genome comparison

Phamerator was written by Dr. Steven Cresawn and has been forked and modified by researchers at Brigham Young University.
Instructions for accessing the original Phamerator code can be accessed at http://phagesdb.org/Phamerator/faq/.

The following zipped file can be downloaded and contains an example database: terminasephages.sql.

This database is organized with phages grouped into clusters based on their DNA packaging strategies. The database demonstrates that large terminases naturally fall into phamilies together with other large terminases of phages using the same packaging strategy. This database is the same one used and referred to in our recent publication:

BD Merrill, AT Ward, JH Grose, S Hope (2016) Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies. BMC Genomics (in press).