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?