How to convert Mauve (xmfa) in Mega, multifasta, phylip or nexus?

Question

[lessismore]

Dear all,

do you know how to convert a mauve alignment in one of these formats?

Thanks in advance

Answer 1

[iraun]

I've not tried but you can use the script available here: http://www.bioperl.org/wiki/Converting_alignment_files

Or also here you have an online tool for conversion (http://www.ibi.vu.nl/programs/convertalignwww/. Try to upload your file and select the input/output formats.

Answer 2

[Charles Warden]

If the goal is to make a tree, I believe Mauve produces a guide tree that is in Newick format. You can use the 'ape' package in R to plot a tree specified in that format.

Otherwise, I haven't tried to convert the raw alignment files.

[jeccy.J]

Is this tree reliable? Does it any model based tree and use bootstrapping?

[kamiljaron]

Quotation form manual of Mauve:

Neighbor joining is then applied to the matrix of distance estimates to yield a guide tree topology. Note that the guide tree is not intended to be a phylogeny indicative of the genealogy of input genomes. It is merely a computational crutch for progressive genome alignment.

So no, it is not reliable tree and it is not using any bootstraping method...