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Old 08-05-2013, 01:11 PM   #5
NGS group
Location: Netherlands

Join Date: Apr 2013
Posts: 28

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?


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 ( or ProgressiveMauve (, filter for blocks that are common to all genomes, then infer a phylogeny from the concatenated alignment? Is that what you had in mind?

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