Hi Michael,
You might check the old archives for this mailing list. The guide tree has been
a hot topic. Here is an excerpted reply from Aaron two months ago:
Re: [Mauve-users] Guide tree question
From: Aaron Darling <darling@cs...> - 2015-12-08 19:32:34
Attachments: Message as HTML
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
See above discussion at:
http://sourceforge.net/p/mauve/mailman/message/34680079/
Full list archives at: http://sourceforge.net/p/mauve/mailman/mauve-users/
Search for “guide tree”
Take care,
Mark
------------------------------
Mark J. Mandel, Ph.D.
Assistant Professor
Department of Microbiology-Immunology
Northwestern University Feinberg School of Medicine
320 E. Superior St., Searle 3-403
Chicago, IL 60611
m-man...@northwestern.edu
http://labs.feinberg.northwestern.edu/mandel/
(312) 503-4138 Office
(312) 503-2915 Lab
(312) 503-9594 Fax
On February 3, 2016 at 9:25:09 AM, michael.sch...@agroscope.admin.ch
(michael.sch...@agroscope.admin.ch<mailto:michael.sch...@agroscope.admin.ch>)
wrote:
After running progressiveMauve I get the usual guide tree which I want to draw
as a Figure. No problem, so far so good…
But in the case of mauve, how to interpret the branch lengths (or the
corresponding numbers)? Normally this is the base changes in percent, as far as
I understand. Does it have the same meaning for Mauve?
Sry, but could not find this info otherwise. If someone can point to a place
where this is documented, would be great!
Michael
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