[Bioperl-l] Converting newick to nexus

Jason Stajich jason.stajich at gmail.com
Thu Sep 19 18:15:19 UTC 2013

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.


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
> --
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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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