PhasomeIt – identification and classification of SSR-mediated PV loci

PhasomeIt is a software tool for identifying and grouping phase variable loci in a group of genomes. It identifies PV loci based on the presence of short simple sequence repeats (SSRs) (found using Bossref) and then uses BLAST to group the loci present in all genomes into homology groups. It will then output this data into HTML format (see here for an example output for Campylobacter). PhasomeIt is written in Python (version 3.3.5 or above) but requires Bossref to function and the BLAST+ suite installed to run from the default path. The BioPython and NatSort python packages are also required.

PhasomeIt can be downloaded from here (version 1.1.1, earlier versions are available on request).

Bossref for Windows and Linux is included in the download, but requires a 64-bit Intel-compatible processor. Note that when running on Linux you may need to set the executable permission bit on the ‘bossref’ file included in the download for it to function.

Citation

Publication is currently in preparation.