How to parsing mugsy (.maf) alignment output to RaxML input

Question

[jeccy.J]

Hi all,

I was trying to run a phylogeny using RaxML of few bacterial genome. I have generated the alignment file using mugsy and convert .maf to phylip using Bioperl. Now the problem is mugsy alignment generated a multiple block local alignment not a global alignment file. Can anyone help me how can I convert that multi block alignment to single global alignment file. To run mugsy I used the command bellow

$mugsy --directory /data/output --prefix mygenomes genome1.fasta genome2.fasta genome3.fasta ..

Thanks advance.

Answer 1

[rafa.rios.50]

To do that I used biopython, which has a module that is not in the main distribution yet, the module is MafIO and with the module AlignIO you can convert from maf to phylip.