BIOCARTA is a web-based, user contributed collection of pathways and the tools to study them. Observe how genes interact in dynamic graphical models

Cell Illustrator is a biopathway modeling and simulation tool

Cognia Molecular is a tool for managing biological information.

GenMAPP (Gene Map Annotator and Pathway Profiler), is a computer application designed to visualize gene expression data on maps representing biological pathways and groupings of genes.

KEGG (The Kyoto Encyclopedia of Genes and Genomes) is a resource for metabolic pathways and regulatory pathways.

LION Target Engine(™) is a suite of programs for pathway and sequence analysis.

MetaCore is an integrated software suite for functional analysis of microarrays, SAGE, proteomics and other experimental data

Multifactor Dimensionality Reduction (MDR) is an open-source, freely available, and user-friendly software package for detecting and characterizing epistasis or gene-gene interactions in genetic and epidemiologic studies of common human diseases.

PathArt is a dynamic pathway articulator, which builds molecular interaction networks from curated databases

PathwayStudio (formerly PathwayAssist) is a powerful, user-friendly software package that allows you to build, visualize and explore biological association networks (BAN)

Pathways Analysis is a web-based application that makes use of Ingenuity Systems' Pathways Knowledge Base, a curated database of millions of modeled relationships between proteins, genes, complexes, cells, tissues, drugs and diseases.

The Pathway Tools software is a bioinformatics software system for pathway analysis of genomes, and for creating Pathway/Genome Databases (PGDBs)

Protein Networker enables an institute to make high throughput protein interaction data

Vector Xpression and Vector PathBlazer is a combined microarray and pathway analysis tool from Invitrogen. Vector PathBlazer software allows you to view protein-protein interactions