Extracting Core Bacterial Genome From Mugsy Alignment

Question

[musta1234]

I recently aligned 60+ 2.2Mb Neisseria genomes using mugsy and need to extract alignment blocks (LCBs) shared by all genomes. Can anyone suggest the best way to get that from a .maf file?

Answer 1

[HG]

You can use Gblocks

http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentation.html#Quick%20Start

Answer 2

[biotech]

I'm in the same boat.

Bernardo