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Old 08-05-2013, 01:11 PM   #5
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Hi Jason,

Thank you for your reply. I am working with 15-20 genomes, which have been assembled. I am using Mauve now, but I think it is not easy to filter the common sequences by manual in Mauve. Do you mean that I just concatenate all common sequences by copy paste? Which alignment and phylogenetic tools are you going to use afterwards? Also Mauve?

Victor

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Originally Posted by themerlin View Post
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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