I am aligning bacterial draft genomes to a reference genomes using mugsy v1.2.3, and I'm using the branch of Biopython that supports MAF files to parse the output and convert to other alignment formats (fasta, nexus).
I've run into a couple problems: 1) In some of the blocks the alignment is to the negative strand of the reference sequence. I think I've solved this problem by identifying those blocks and using Biopython's reverse complement feature to change all the sequence records in that block. 2) It appears that some of the blocks overlap each other in reference to the positions in the reference sequence. This becomes a problem when I try to create a MAF index to help convert to other formats.
Is there any way to specify a particular sequence as reference with mugsy? Anyone have any tools they would recommend to deal with the overlapping blocks?