FORRepeats: detects repeats on entire chromosomes and between genomes
Towards a computational model for – 1 eukaryotic frameshifting sites
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks
‘Hybrid Protein Model’ for optimally defining 3D protein structure fragments
Discovering well-ordered folding patterns in nucleotide sequences
LTR_STRUC: a novel search and identification program for LTR retrotransposons
Identifying differentially expressed genes using false discovery rate controlling procedures
Multifactor dimensionality reduction software for detecting gene–gene and gene–environment interactions
GenePath: a system for automated construction of genetic networks from mutant data
SimiTri—visualizing similarity relationships for groups of sequences
A literature-based method for assessing the functional coherence of a gene group
Identification of key concepts in biomedical literature using a modified Markov heuristic
The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks
cMap: the comparative genetic map viewer
IslandPath: aiding detection of genomic islands in prokaryotes
Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP
MELINA: motif extraction from promoter regions of potentially co-regulated genes
AltAVisT: Comparing alternative multiple sequence alignments
PCMA: fast and accurate multiple sequence alignment based on profile consistency
PDP: protein domain parser
pathSCOUT™: exploration and analysis of biochemical pathways
KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data
Modeling biological systems using Dynetica—a simulator of dynamic networks
GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs
WiGID: wireless genome information database
Wrapping up BLAST and other applications for use on Unix clusters