phylip format from Mummer

Question

[micro32uvas]

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

Answer 1

[ALchEmiXt]

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.