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>
> 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
>
> 706-542-5859
>
>
>
>
>
>
>
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