BioPAXViz
Computational Tool
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General Information
DescriptionA cytoscape application for the visual exploration of metabolic pathway evolution
Homepagehttps://github.com/CGU-CERTH/BioPAX.Viz
Publications
BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution
Fotis E. Psomopoulos; Dimitrios M. Vitsios; Shakuntala Baichoo; Christos A. Ouzounis
Summary: 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.
Availability and Implementation: 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.
Contact: ouzounis@certh.gr.
DOI: https://doi.org/10.1093/bioinformatics/btw813
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