Names on Nodes: Java Toolkit
Names on Nodes is an application that automates the application of biological nomenclature to phylogenetic datasets.
The project website has more information.
This repository is for the Java Toolkit associated with the project. This toolkit may be used as a basis for a command-line or server-based tool.
This version will be capable of reading phylogenetic hypotheses (modeled as directed, acyclic graphs) from a variety of file formats (MathML, NEXUS, nexml, GraphML, etc.). Phylogenetic hypotheses can then be paired to dictionaries of declarations, which tie names to mathematical definitions. The pairing of a phylogenetic hypothesis and a declaration dictionary provides a "context", which may be loaded from a MathML file. Labelled phylogenies can then be exported in a variety of formats.
Names on Nodes: Java Toolkit is being developed using Java Development Kit 6 and JGraphT.