Phylogenetic Visualization Software on the NetBeans Platform
By Geertjan-Oracle on Apr 20, 2013
With decreasing DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. Phylogenetics is the study of evolutionary relationships among groups of organisms (e.g., species, populations), which are discovered through molecular sequencing data and morphological data matrices. Phyloviz, a phylogenetic visualizer, is software that is being created, primarily in Portuguese academic institutions, to analyze sequence-based typing methods that generate allelic profiles and their associated epidemiological data.
For representing the possible evolutionary relationships between strains identified by allelic profiles it uses the goeBURST algorithm, a refinement of eBURST algorithm proposed by Feil et al., and its expansion to generate a complete minimum spanning tree (MST). The software uses the Prefuse and Freehep libraries for data visualization. The software is being developed in a modular way, i.e., on the NetBeans Platform, to allow its expansion with novel data analysis algorithms and new visualization modules.
The application is actively being worked on by developers from a variety of institutions in Portugal:
- Molecular Microbiology and Infection Unit of the Faculty of Medicine, University of Lisbon
- Computer Engineering Department of the Technical University of Lisbon
- Telecomunications, Electronic Engineering, and Computers Department Polytechnic Institute of Lisbon
- Knowledge Discovery and Bioinformatics team of INESC-ID, Lisbon
A number of plugins have been created for Phyloviz:
Finally, YouTube has a few nice screencasts about Phyloviz, with cool accompanying music: