Hello Berthold,
On Mon, 2014-08-11 at 13:34 +0200, heinze wrote:
> genes (as per the GenBank file annotation). However, the exported file
> just lists the coordinates of the GenBank genome, without any sign of
> comparing to the second, fasta sequence. This is regardless of which
> features I sel
Hi Saleh, I realize this reply is coming quite late. Hopefully it is
still useful. more below...
On Wed, 2014-06-18 at 09:43 +1000, Saleh T wrote:
> I used progressivemauve to compare two genomes each saved in the fasta
> file format. In each genome file there are more than one sequence
> corresp
Hi Manal,
The first two steps outlined on this page provide one example for how a
collection of genomes can be aligned and from them a phylogeny inferred:
http://code.google.com/p/clonalorigin/wiki/FromGenomeAssemblyToRecombination
Best,
-Aaron
On Tue, 2014-06-17 at 19:13 +1000, Manal Farid wrote
Hi Tina, this appears to be a bug in the Mauve snapshot you are using.
Would you be able to provide me with a copy of the sequence files &
alignment so I can track down the problem and fix it? In the meantime,
if you obtain the 2.3.1 release version from here:
http://gel.ahabs.wisc.edu/mauve/downlo
Hi Bhav,
A handful of things changed in the implementation of library functions
during the development of progressiveMauve (the main new feature in the
2.x release series) that also changed mauveAligner (because they use
some of the same library functions). I don't have a summary of the
details of
Hi Cristina,
Mauve uses a GenBank sequence file parser implemented in BioJava 1.7,
which is somewhat strict & brittle in its interpretation of the format.
If you can provide the error messages that appear in the Mauve console
log when you load the alignment then myself or someone else on the list
m
Hi Jonas, this is an issue that's specific to the Java VM that you're
using. I just wrote a separate message about it but the short story
workaround is that if you can switch to the Sun VM the problem should go
away.
On Wed, 2014-06-25 at 00:57 +1000, Jonas Torgny Larsson wrote:
> Dear all,
>
> I
Hi Julie, apologies for the delayed response.
Matt DeMaere here at UTS has looked into this issue and it appears to be
a problem specific to recent versions of OpenJDK. Whereas the code will
work command-line on the Sun Java VM without an X11 environment, the
OpenJDK implementation of Java library
Hi Carmela, apologies for the delayed response.
Without seeing the exact details of what you're observing, e.g. with a
screenshot, it's hard for me to know whether this is actually a bug or
some confusion in the interpretation of how the viewer displays the
alignment. Just to clarify a bit: the XMF
Hello all
I am having problems exporting orthologs after progressiveMauve alignment of
two plant mitochondria, a GenBank file and a fasta sequence, each of them <1Mb.
I see nice LCBs, many of which contain genes (as per the GenBank file
annotation). However, the exported file just lists the coo
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