[Tdwg-phylo] Publishing a trees in RDF

Christian M Zmasek czmasek at sanfordburnham.org
Thu Oct 21 18:57:09 CEST 2010

Hi, Dave and Rutger:

My own tree viewer "Archaeopteryx" provides such an overview when zoomed 
in, plus some other features described as "missing" in most current tools.

See: http://www.phylosoft.org/archaeopteryx/

Example: http://www.phylosoft.org/archaeopteryx/examples/mollusca.html

Archaeopteryx also provides other useful features (at least for 
comparative genomics use cases). For example, the ability to infer 
internal taxonomies (if all external nodes have _some_ taxonomic 
information associated with them; standalone version only; via uniprot 
taxonomy database).

Please let me know if you'd like to know more or have suggestions for 
improvement (although keep in mind that this Archaeopteryx is just a 
peculiar hobby of mine).


On 10/21/2010 3:39 AM, Rutger Vos wrote:
> Hi Dave,
>> The ability to browse large trees seems to be a particular limitation of existing tools (I'd love to be corrected if I am wrong). Having a tree larger than the widget, as in Phylowidget, is one approach, however, an overview window would be nice to orientate your view in relation to the entire tree. I have also been considering displaying only a subset of nodes and then having 'expand', 'contract' and 'pan' (by expanding and contracting) functions for navagation. The ability to display node subsets is probably more important for networks than trees as reticulation will often result in visual occlusion.
> Rod Page has coded a web widget (I believe all javascript) that has a
> small preview window for the whole tree and a larger "zoomed in" view.
> "TreeJuxtaposer" is a java app(let?) that allows you to contract and
> expand selections of nodes/clades. I think these come closest to what
> you are talking about, though neither operates on networks.
> Cheers,
> Rutger

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