Hilmar Lapp | 20 Sep 02:36 2013

Re: Converting newick to nexus

There's also Bio::Phylo (http://search.cpan.org/dist/Bio-Phylo/) which you might try for your
purpose. I'm copying its author, Rutger Vos, who I was possibly erroneously assuming to be on the list.


On Sep 19, 2013, at 2:15 PM, Jason Stajich wrote:

> Johan -
> I worry that this really won't be best solved in Bio::TreeIO tree modules which are really written around
streaming trees through not writing into a compact format which pretty much requires having the whole set
of trees in memory. 
> There are other efforts like Bio::Nexus (http://sourceforge.net/projects/bionexus/) which could
solve it better as it is intended to deal with the Nexus format more completely, what we handle in
Bio::TreeIO .
> But that isn't to say someone couldn't try and work on it for Bio::TreeIO parser. I personally have no
bandwidth for this at the moment but maybe it can be written into a project idea for the bioperl wiki to
recruit someone to work on it.
> Jason
> On Sep 17, 2013, at 1:21 PM, nylander <Johan.Nylander <at> abc.se> wrote:
>> Dear Jason,
>> Unfortunately, this issue is perhaps a bit more complicated than just
>> omitting the nexus header ('#NEXUS') after the first tree is printed. As
>> soungalo pointed out, both the header AND the translation table is repeated
>> for every tree. This makes the output file larger than (perhaps) necessary.
>> Optimally (and I think this is what soungalo wanted), the output should
>> contain only a single translation table, and all trees should be written to
>> the same tree block (cf. the output from phylogenetic MCMC software MrBayes,
>> PhyloBayes, etc). This is only possible if all trees contain the same tip
>> labels. Hence, all trees needs to be checked before the trees can be printed
>> in a single tree block. As implemented now, each translation table is
>> created by parsing the order of tip labels in each individual tree. This
>> makes sense if the trees might differ in size and/or labels. But again, if
>> we have many thousands of trees with the same set of tip labels, repeating
>> the translation table should be avoided.
>> I know that an efficient and "optimal" (see above) nexus tree writer is
>> wanted by many, but I'm unsure how much effort that is involved in order to
>> handle the multi tree issue.
>> Yours
>> Johan
>> --
>> View this message in context: http://bioperl.996286.n3.nabble.com/Converting-newick-to-nexus-tp17013p17153.html
>> Sent from the Bioperl-L mailing list archive at Nabble.com.
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> Jason Stajich
> jason.stajich <at> gmail.com
> jason <at> bioperl.org
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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :