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Old 09-04-2012, 10:02 AM   #4
themerlin
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Location: Flagstaff, AZ

Join Date: Feb 2010
Posts: 51
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I'm not sure that you can create a tree from a MAF file with overlapping reads. With Mugsy, you usually provide separate files for each genome and then infer a tree from sequence conserved in each block. If you can get your MAF file in this format, you can create a FASTA alignment with Galaxy or with scripts in the bx-python package (https://bitbucket.org/james_taylor/bx-python/wiki/Home).
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