Hi there, I'd like to get a human-chimp-mouse genome alignment, but from the UCSC database, I didn't find appropriate multiple alignment for my need (multiple alignments here seem to contain a lot of species). So I am trying to align these genomes locally using multi-Z tool. My question is: should I put all the chromosomes from a species in a single file and run the multi-z program? It seems to take forever to finish this, is there any quick way to do this? On the UCSC database, the multiple alignment data are chromosome by chromosome, what should I do if I want a result like that? Your help will be appreciated!
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