[Biopython-dev] [Bug 2552] Adding alignments

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2552





------- Comment #2 from fkauff at biologie.uni-kl.de  2008-11-13 02:16 EST -------
The Nexus module in Bio.Nexus has a function (not a method) 'combine' that can
combine Nexus objects. It takes care of missing taxa, taxon sets, etc. Usage is
something like:

nex1=Nexus.Nexus('myfirstalignment.nex')
nex2=Nexus.Nexus('mysecondalignment.nex')
combined=Nexus.combine([('fancyname1',nex1),('fancyname2',nex2)])

It looks fairly straightforward to add this to a SeqRecord object.

Cheers,
Frank

(Hi Cymon)



(In reply to comment #1)
> (In reply to comment #0)
> > This is related to the very broad alignment bug 1944.
> > 
> > Given two alignments, it can make sense to talk about adding them together.
> 
> Actually, this is a very common procedure in phylogenetic analyses, where
> multiple genes/loci are combined into a "super" matrix for a set of taxa.
> Although, in this case, adding by column, if a taxon/row/identifier was missing
> in a particular (sub-)alignment it would be filled by "-" (missing data) in the
> combined matrix.
> 
> Anyway, I think this would be a very useful enhancement.
> 


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