Dear UCSC, I want to do multiple alignment among human(hg19), gibbon(nomLeu1) , marmoset (calJac3) and cow (bosTau6), using multiz. To get a proper whole genome alignment, usually synNet or reciprocalBest pairwise alignment with human is used. Most of the time, you have already given us the alignment files in UCSC(Thanks a lot for that). But for gibbon, marmoset and cow, neither of the two alignment format is given. So which kind of the pairwise alignment method is better for the three species I mentioned above? Plus: The sequencing coverage is 5.6X for gibbon, 6X for marmoset. I don't know the sequencing coverage for cow. Sincerely, Chen Ming
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