  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. The software creates and manages a type
of organism-specific database called a Pathway/Genome Database (PGDB), which
the software enables database curators to interactively edit. It supports web
publishing of PGDBs and provides a large number of query, visualization, and
omics-data analysis tools. Scientists around the world have created more than
9,800 PGDBs by using Pathway Tools, many of which are curated databases for
important model organisms. Those PGDBs can be exchanged using a peer-to-peer
database-sharing system called the PGDB Registry.
