Convert .Maf To .Xmfa Alignment?

Question

[anin.gregory]

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!

Answer 1

[Hamish]

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.