Microarray Analysis

• MeV, an all-in-one microarray visualization and clustering kit.
• Java TreeView, the standard for microarray visualization, hierarchical clustering, and copy number analysis.
• Cluster, a quick-and-dirty hierarchical clustering program that produces TreeView-compatible output.
• Expander, a clustering program mainly useful for its implementation of the SAMBA biclustering algorithm.
• GeneXPress, relatively outdated microarray analysis software.

Graph Visualization

• Graphviz, AT&T software for static graph rendering. Scales up to ~100-200 edges, anything bigger looks like a hairball.
• Cytoscape, bioinformatics-specific tool mainly used for pathway visualization. Behavior varies; great for very small networks, passable up to a few hundred edges, anything bigger looks like a hairball.
• OpenJGraph, an outdated but open-source and free Java graph interaction package.
• JGraph, an up-to-date but semi-commercial Java graph interaction package.

Bayesian Networks

• GeNIe and SMILE, Bayesian network construction, visualization, and inference tools from the University of Pittsburgh.
• BNT, a Matlab Bayesian parameter and structure inference package.
• PNL, a crufty and difficult to use Bayes Net library from Intel with the major benefit of being open source.

Binding Site Analysis

• FIRE, superb mutual-information based sequence motif discovery from Saeed's lab.
• CREME, regulatory motif and module discovery using sequence enrichment and evolutionary conservation.
• MEME, moderately crummy but standard discovery of enriched motifs in a set of input sequences.
• MDscan, motif discovery based on ChIP-chip data.

Other

• BioMart, a massively useful tool for gene cataloging, ID interconversion, sequence retrieval, and more.
• Entrez, cross-organism gene lookup.
• SVM Light, quick and easy Support Vector Machines.
• WEKA, very general, convenient, and comprehensive machine learning package.
• Gene ID Converter, human gene ID interconversion.