BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution.

Abstract

BioPAXViz is a Cytoscape (version 3) application, providing a comprehensive framework for metabolic pathway visualization. Beyond the basic parsing, viewing and browsing roles, the main novel function that BioPAXViz provides is a visual comparative analysis of metabolic pathway topologies across pre-computed pathway phylogenomic profiles given a species phylogeny. Furthermore, BioPAXViz supports the display of hierarchical trees that allow efficient navigation through sets of variants of a single reference pathway. Thus, BioPAXViz can significantly facilitate, and contribute to, the study of metabolic pathway evolution and engineering. BioPAXViz has been developed as a Cytoscape app and is available at: https://github.com/CGU-CERTH/BioPAX.Viz. The software is distributed under the MIT License and is accompanied by example files and data. Additional documentation is available at the aforementioned GitHub repository. ouzounis@certh.gr.