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 h
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 - 2015-12-08 19:32:34
Attachments: Message as HTML
The vagueness in that file
Hi,
I have aligned 5 bacterial genomes using the progressiveMauve. I would like
to extract the part of the alignment having sequence in all the genome (eg:
second and fourth line positions) using the alignment(.xmfa) file and
backbone(.backbone) file.
seq0_leftend seq0_rightend seq1_leftend seq1
Hi Gopi,
If I understand you correctly, you are trying to extract the LCBs from your
alignments. I used the stripsubsetsLCB command to do this with the genomes I am
working with. The only issue I had was that if you ran your alignment in the
Windows GUI and not using Linux then the path names
