Thank you for all of your helpful responses. I guess at this point my question
changes. I would like to build a phylogenetic tree of this alignment and I
assume I need to convert the XMFA file to another format to complete this task.
Has anyone had experience with file conversion and what program would you
recommend for phylogenetic tree reconstruction? At present I am using MEGA6
but I think these files are too big for that program to run effectively.
Thanks,
Susan
From: Aaron Darling [mailto:darl...@cs.wisc.edu]
Sent: Tuesday, December 08, 2015 2:32 PM
To: mauve-users@lists.sourceforge.net
Subject: Re: [Mauve-users] Guide tree question
The vagueness in that file is at least partially intentional -- the tree
doesn't have a well-established interpretation outside of being a reflection of
the order in which genomes were aligned. I think it would be dangerous to
interpret it as a phylogeny, especially as one intended to represent vertical
inheritance, as the topology is shaped heavily by gene content and there are
well documented cases where independent lineages have converged in gene content
(e.g. Shigella) and I've seen the guide tree and phylogeny conflict strongly in
such datasets.
Best,
-Aaron
On Tue, 2015-12-08 at 14:09 -0500, Amarin Cogburn wrote:
As far as I know there is no way to have the file/sample names appended to the
guide tree. The sequence order is the order in which the files were added in
the alignment setup. I've been manually changing the seq names in the guide
tree file. If there is another way of doing it I'd love to hear it as it does
get cumbersome when you have more than a handful of sequences.
On Tue, Dec 8, 2015 at 12:29 PM, Susan Beth Fogelson
<foge...@uga.edu<mailto:foge...@uga.edu>> wrote:
Hello,
I used progressive mauve to align 32 genomes, which produced a guide tree file.
When I opened this file in Geneious the labels on the tree are not my original
sequence labels. The new labels just say seq 1, seq 2, seq 3, etc up to seq
32. I was wondering if there is a way to visualize my original sequence labels
on this tree?
-Susan
Susan Fogelson, DVM, MS, Dipl. ACVP
Aquatic Animal Anatomic Pathologist and PhD candidate
foge...@uga.edu<mailto:foge...@uga.edu>
706-542-5859<tel:706-542-5859>
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