Re: [Treebase-devel] remedying mismatched OTU names

[Rutger V. <R....@re...>]

> this calls for easy-to-use NeXML editors. e.g. add the ability to enter
> Genbank accession numbers in Mesquite, and then save as NeXML, thus
> preserving "Homo_sapiens" consistently in all alignments and resulting
> trees, while still communicating the respective accession numbers for each
> locus. Summer-of-Code project here.

Indeed.

> C- The basic data model of matrix-rows-matching-with-tree-OTUs works for 99%
> of datasets, but a growing number of studies use BEAST species inference
> (and other similar methods) where the tree ends in species OTUs, but the
> alignment has many more haplotype OTUs. -- i.e. there is, on purpose, a
> complete mismatch between alignment row labels and tree OTUs. Mesquite can
> handle this using a taxon association table, though I don't know that this
> is formal NEXUS or just a Mesquite invention. I don't think that NeXML or
> PhyloML can handle this. This calls for expanding the capabilities of NeXML
> and PhyloML.

Yes and no. Multiple matrix rows can reference the same otu, but
that's not quite what we want. Multiple, separately annotatable matrix
row segments would be a good feature to have, also for TreeBASE's
needs.



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading, RG6 6BX, United Kingdom
Tel: +44 (0) 118 378 7535
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