phylip format from Mummer
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5.2 years ago
micro32uvas ▴ 10

Hello Everybody,

I have aligned my bacterial genomes using run-mummer 3, but the output formats: .align .out. .gaps .errorgaps

Now, I want to draw phylogenetic tree using PHYLIP but cannot find the appropriate way / format for that. Your help would be greatly acknowledged.

Qurat

phylip run-mummer 3 phylogenetic tree • 1.3k views
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5.2 years ago
ALchEmiXt ★ 1.9k

First thing you have to do is to convert the pair-wise MUMmer output into a distance metric. I have very good experience with the MUMi distance (as explained in this paper). Using that distance between pairwise alignments you can build a distance matrix on which you can perform for instance the BioNJ algorithm using Splitstree. From there you can also export if still necessary.

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