For example, I want to perform multiple genome alignment for cat, dog and cow using lastz. How should I specify the argument to run alignment for all of them?
Or should I run pairwise lastz and then combine the results? If so, how should I do?
Lastz is a pair-wise aligner.
Have you looked at the pre-computed alignments from UCSC (scroll down the page and find multiple-alignments) or Ensembl (these are pairwise alignments with synteny analysis for some) for vertebrate genomes?
Pre-computed alignments are not available for domestic water buffalo (Bubalus bubalis) in UCSC or ensemble. I want to create a maf file for buffalo with human, cow and dog. Is there any tutorial links on how to perform multiple alignment on genomes? What may be memory requirement to do the same?
Do you find any solution or option to do the same?
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