[Treebase-devel] NEXUS output problems

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

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


PS: You can add my name to the list of people who would appreciate a link to a full dump of the DB whenever it is available.