Before trying anything and running into trouble, I'd suggest you read comparisons between the available programs, like these recent papers:
- Vernikos, G., Medini, D., Riley, D. R., & Tettelin, H. (2014). Ten years of pan-genome analyses. Current Opinion in Microbiology, 23C, 148–154. doi:10.1016/j.mib.2014.11.016
- Xiao, J., Zhang, Z., Wu, J., & Yu, J. (2015). A Brief Review of Software Tools for Pangenomics. Genomics, Proteomics & Bioinformatics, 13(1), 73–6. doi:10.1016/j.gpb.2015.01.007
I use both Spine/AGEnt (DNA- based) and Roary (protein- based). Roary is especially useful if you're annotating novel genomes with Prokka, as it takes the Prokka's GFF output directly as input, without any conversions in between.
I think PGAP is one of your option. But I'm not sure whether it will be working standalone PC though.
Bioinformatics. 2012 Feb 1;28(3):416-8. doi: 10.1093/bioinformatics/btr655. Epub 2011 Nov 29. PGAP: pan-genomes analysis pipeline. Zhao Y1, Wu J, Yang J, Sun S, Xiao J, Yu J.