Extracting Core Bacterial Genome From Mugsy Alignment

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?

alignment maf

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updated 12.0 years ago by HG

• written 13.0 years ago by musta1234 •

2 answers

You can use Gblocks

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

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written 12.0 years ago by HG

I'm in the same boat.

Bernardo

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written 13.0 years ago by biotech

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