Question

Extracting Core Bacterial Genome From Mugsy Alignment

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10.7 years ago

musta1234 ▴ 30

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 • 3.1k views

ADD COMMENT • link updated 9.7 years ago by HG ★ 1.2k • written 10.7 years ago by musta1234 ▴ 30

score 2 · Answer 1 · 2014-08-01

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9.7 years ago

HG ★ 1.2k

You can use Gblocks

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

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score 0 · Answer 2 · 2013-07-31

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10.7 years ago

biotech ▴ 570

I'm in the same boat.

Bernardo

ADD COMMENT • link 10.7 years ago by biotech ▴ 570