Question: Convert .Maf To .Xmfa Alignment?
0
gravatar for anin.gregory
5.9 years ago by
anin.gregory80
United States
anin.gregory80 wrote:

Hi I am trying to use the Clonal Origin pipeline (https://code.google.com/p/clonalorigin/wiki/FromGenomeAssemblyToRecombination) and because I have so many genomes running progressiveMauve took too long. As a result, I used Mugsy and got a .maf output. For the pipeline, I need a .xmfa output. Does anyone know a way to convert from .maf to .xmfa?

I wanted to use Bioperl Align::IO, but it does not support maf. Suggestions?

Thanks!

maf alignment convert • 3.1k views
ADD COMMENTlink modified 5.9 years ago by Hamish3.1k • written 5.9 years ago by anin.gregory80
3
gravatar for Hamish
5.9 years ago by
Hamish3.1k
UK
Hamish3.1k wrote:

According to the BioPerl HOWTO:AlignIO and SimpleAlign document Bio::AlignIO can read (but not write) MAF, and write (and read) XMFA. So since you want to convert from MAF to XFMA it should work.

From a couple of quick Google searches is appears that Mauve has programs for converting between MAF and XMFA as part of the source code (maf2xmfa & xmfa2maf), oddly these do not appear in the binary distribution. See the Mauve developer documentation for details of how to build Mauve from source.

ADD COMMENTlink written 5.9 years ago by Hamish3.1k
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