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....