I am using lastz to align two genomes. I found there are some regions in genome A aligned to two regions in genome B. I want to find out the alignment with the best quality. How should I deal with that? Can I keep both alignments?
Here are the detailed steps http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto
Login before adding your answer.
Use of this site constitutes acceptance of our User Agreement and Privacy