[Biopython] Nexus format dialects in Biopython

[Lior Glick]

Dear list members,
I'm trying to convert newick formated trees to the nexus format. I'm doing
this since I'd like to use the trees as input for a software (BayesTraits
V2) which will only accept nexus trees. It also required that the file is
in a specific dialect of nexus in which the taxa names are translated to
numbers, and the trees themselves only contain these numbers.

I tried
Bio.Phylo.convert(newick_trees_file,'newick',nexus_trees_file,'nexus'), but
it produces nexus files with the taxa names within the trees. I couldn't
find out a way to control the specific dialect of nexus to be used. Looking
into the Bio.Nexus module wasn't very helpful either.

Does anybody know of a way to do that?

Thanks,
Lior
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20140907/61c31592/attachment.html>