I have my work cut out for me....
Names on Nodes: Automating the Application of Taxonomic Names within a Phylogenetic Context
Names on Nodes1 is an open-source2 Flex application which utilizes a mathematical approach to automate the application of phylogenetically-defined names to phylogenetic hypotheses. Phylogenetic hypotheses are modeled as directed, acyclic graphs, and may be read from bioinformatics or graph files (Nexus, NexML, Newick, and GraphML) or created de novo. Hypotheses may also be merged from multiple sources. Names on Nodes stores hypotheses as MathML, an XML-based language for representing mathematical content and presentation. Phylogenetic definitions may be constructed using a visual editor and exported in MathML. Thus, it is possible to create a dictionary of defined names and automatically apply them to phylogenetic hypotheses. In the current version of the application, such dictionaries exist only as MathML files, but in future versions definitions may also be loaded from databases (e.g., RegNum).
Additional functionality in Names on Nodes includes the ability to coarsen a phylogenetic graph (thereby simplifying it while still reflecting the overall structure) or to export it as an image file (raster or vector, potentially with semantic annotations).
- Source code available at: http://bitbucket.org/keesey/namesonnodes-sa/
- MIT license
27 May 2010
Upcoming Names on Nodes Presentation
I'll also be presenting Names on Nodes at iEvoBio, at the Software Bazaar on June 29. Here's the abstract: