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

[Rutger V. <rut...@gm...>]

Bio::Phylo reads LINK and TITLE tags correctly and uses them to link
blocks to one another.

On Fri, Mar 25, 2011 at 6:01 PM, William Piel <wil...@ya...> wrote:
>
> 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
>
>
>
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-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
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