Question: How to parsing mugsy (.maf) alignment output to RaxML input
gravatar for jeccy.J
2.7 years ago by
jeccy.J50 wrote:

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.

mugsy raxml phylogeny • 1.3k views
ADD COMMENTlink modified 2.3 years ago by rafa.rios.5050 • written 2.7 years ago by jeccy.J50
gravatar for rafa.rios.50
2.3 years ago by
rafa.rios.5050 wrote:

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.

ADD COMMENTlink written 2.3 years ago by rafa.rios.5050
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