Re: [Treebase-devel] Fwd: reading nexus file from treebase?

[William P. <wil...@ya...>]

On Mar 25, 2011, at 11:51 AM, Rutger Vos wrote:

> The additions are necessary because they specify the relationships
> between multiple taxa blocks, characters blocks and tree blocks.
> They're not part of the core standard per se, though - I think they
> were introduced by mesquite. Maybe ape should switch to nexml instead?


According to this:

https://www.nescent.org/wg_phyloinformatics/Supporting_NEXUS#Testing_conformance_of_NEXUS_files

Both MacClade and Mesquite are "level III parsers" for validating NEXUS files. Neither has a problem with TITLE and LINK commands. PAUP does not object to them either.  I haven't tested Bio::NEXUS, though, which is the other level III parser that is recommended. 

bp