Re: [Treebase-devel] NEXUS output problems

[Mark H. <mth...@gm...>]

Hi,
	Yes.  That appears to works for my NEXUS parser.

thanks,
Mark


On May 10, 2011, at 4:07 PM, William Piel wrote:

> Hi Mark,
> 
> Could you try our dev server?  Harry recently committed a bug fix for this.
> 
> http://purl.org/phylo/treebase/dev/phylows/study/TB2:S2012
> 
> regards,
> 
> Bill
> 
> On Apr 21, 2011, at 11:09 PM, Mark Holder wrote:
> 
>> Hi,
>> 	I just downloaded S2012.nex (I can send it along if needed, but I won't clutter your inboxes unless it is needed. The url ishttp://purl.org/phylo/treebase/phylows/study/TB2:S2012 ).
>> 
>> 	My NEXUS parser is choking on a couple of things:
>> 		1. The names of the CHARSET commands in the SETS block have spaces, but the names have not been "escaped" to convert them to single NEXUS tokens.  
>> 
>> 		2. There are multiple TAXA blocks but the TREES blocks do not use the LINK command to disambiguate.  Mesquite is smart enough to figure out which TAXA block is correct.  I suppose I could add taxa-block-detection code to NCL (the NEXUS parsing library that I use), but it would be much easier if TreeBase used LINK to clarify the connections.
>> 
>> all the best,
>> Mark
>