Hi Ariadna,

On Tue, 2010-04-27 at 12:18 +0200, Ariadna Rodriguez Chamorro wrote:
> Dear All, 
> I need  the LCB boundary output file which mauve_user_guide(v 2.3.1)
> said is a "file that complements the permutation matrix file with
> information about the LCB boundaries". I thought it was possible to
> obtain it by exporting the "permutations"  but apparently that's not
> enough 'cause I only got the .permutations file and not the LCB
> boundaries one. 
> I will appreciate very much if anyone can give me a hint to output
> this file, I've been looking once and other time through the docs but
> I can't understand what's the missing point. 

The LCB boundary file can be created via command-line tools, but not yet
through the graphical interface.  Sorry for any confusion.

Instructions for generating the LCB boundary file from a
progressiveMauve alignment can be found in step 2 of the instructions on
this page:

Two programs are required: projectAndStrip, and makeBadgerMatrix.  Both
are available for Mac, Windows, and Linux from the "other programs" link
in the "Successful builds" section of this web page:

If you're using linux or mac, don't forget to make the projectAndStrip
and makeBadgerMatrix programs executable before trying to run them; it
can be done with:

chmod 755 projectAndStrip
chmod 755 makeBadgerMatrix

Also, beware that those programs assume the input genomes are a single
chromosome.  Multiple chromosomes/contigs/plasmids will be concatenated
together, which may not be a desirable result depending on what you're
trying to do...

Hope that helps, -Aaron

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