[Biopython-dev] Cookbook entry, concatenating nexus files

Peter biopython at maubp.freeserve.co.uk
Thu May 14 09:27:12 UTC 2009

On Thu, May 14, 2009 at 5:53 AM, David Winter
<winda002 at student.otago.ac.nz> wrote:
> I have been slowly adding some of the scripts I use most commonly to the
> cookbook section of the wiki (http://biopython.org/wiki/Category:Cookbook).
> Since I'm very much a  dilettante at this programming business as the
> cookbook is meant as supplementary documentation for Biopython it's probably
> a good idea for someone that knows what they are doing to look at these
> things (Peter has been really helpful with this thus far, but is seems
> unfair to saddle one man with so much bad programming :)
> I've just added a recipe that uses the nexus class to concatenate multiple
> nexus files and provide some feedback if the taxa are not the same in each
> one: http://biopython.org/wiki/Concatenate_nexus
> Any thoughts? If you think you can make it clearer/quicker/better then you
> can edit it on the wiki or provide comments here of there.

What exactly are you trying to achieve?  A big Nexus files with lots
of alignments (and trees) in it?

When I talked to Frank about Nexus files, he said they should only
ever hold one alignment matrix, hence Bio.AlignIO does not allow
writing multiple alignments to a single Nexus file.  If you have some
real world examples of Nexus files holding more than one alignment
matrix, please share them - then we can try and get Bio.AlignIO (and
if need be Bio.Nexus) to cope with them directly!


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