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Old 08-05-2013, 11:39 AM   #3
themerlin
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Location: Flagstaff, AZ

Join Date: Feb 2010
Posts: 51
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How many genomes are you working with? And are you working with assemblies or raw reads?

For a smaller number of genome assemblies, you could do whole genome alignments with Mugsy (http://sourceforge.net/projects/mugsy/files/) or ProgressiveMauve (http://gel.ahabs.wisc.edu/mauve/), filter for blocks that are common to all genomes, then infer a phylogeny from the concatenated alignment? Is that what you had in mind?

Jason
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