Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

Brief Bioinform. 2016 Sep;17(5):877-90. doi: 10.1093/bib/bbv079. Epub 2015 Oct 10.


Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms.

Keywords: computational genomics; metabolic models; metabolic pathways; systems biology.

MeSH terms

  • Computational Biology
  • Genome*
  • Genomics
  • Internet
  • Metabolic Networks and Pathways
  • Software Design
  • Systems Biology