Saturday Apr 20, 2013

Phylogenetic Visualization Software on the NetBeans Platform

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:

A number of plugins have been created for Phyloviz:

http://www.phyloviz.net/wiki/plugins/

Finally, YouTube has a few nice screencasts about Phyloviz, with cool accompanying music:

About

Geertjan Wielenga (@geertjanw) is a Principal Product Manager in the Oracle Developer Tools group living & working in Amsterdam. He is a Java technology enthusiast, evangelist, trainer, speaker, and writer. He blogs here daily.

The focus of this blog is mostly on NetBeans (a development tool primarily for Java programmers), with an occasional reference to NetBeans, and sometimes diverging to topics relating to NetBeans. And then there are days when NetBeans is mentioned, just for a change.

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