DNASTAR
	DNASTAR Homepage—Commercial company with many pieces of software related to sequence analysis including primer design, sequence assembly, protein structure predictions, and alignments

	Genomatix Suite
	Genomatix Inc. Homepage—Commercial software capable of searching genomic sequence data for specific transcripts, loci, and the like as well as performing analyses related to promoters, transcription factor binding sites, and general sequence analysis; provides demos and some free access

	MADIBA
	MADIBA Sequence Alignment Software from the University of Maryland Biotechnology Center—A software package from the alignment of nucleotide and protein sequences

	pDRAW32
	pDRAW32 Homepage—Freeware software designed to do simple sequence analysis but is also capable of storing annotation information, primer, information, and vector design information as well as perform restriction enzyme predictions and simulate gel results

SEQtools

SEQtools by Søren Rasmussen—SEQtools 8.2 is a comprehensive win32 program package for handling and analysis of nucleotide and protein sequences. The program includes a series of trivial functions to help you carry out common operations. In addition SEQtools will assist you with more demanding tasks like unattended batch blast search at NCBI with advanced facilities for retrieving, storing and listing search results

	Sequencher
	Sequencher DNA Analysis software from the Gene Codes Corp.—Commercial software capable o f sequence alignments and assembly as well as annotating sequences and performing RE and ORF predictions

	TIGR Analysis Software
	Seqeuence Analysis Software from TIGR—Numerous free software programs designed for gene discovery, gene annotation, gene prediction, gene alignment and various permutations

	Vector NTI
	Vector NTI from Informax—Vector NTI Advance is the most robust and highly integrated application available in the market for desktop sequence analysis and molecular biology data management

	Acuity
	Acuity from Axon Instruments—A data storage and analsis software suite that works alongside GenePix; normalization, filtering, and clustering as well as some data management

	Affymetrix
	Affymetrix, Inc. Homepage—Makers of the GeneChip oligonucleotide microarray platform as well as Microarray Suite, GCOS, and DMT analysis applications for the GeneChip platform

	AMAD
	AMAD written by Dr. Joe DeRisi—Another Microarray Database: Perl scripts for managing microarray data on flat files

	ArrayDB
	ArrayDB from NHGRI/NIH—ArrayDB 2.0 is a software suite that provides an interactive user interface for the mining and analysis of microarray gene expression data. All of the analyzed expression data from a microarray experiment, as well as information about the clones used in the experiment, are stored in a relational database

	arraystats
	arrraystats written by Paul Pavlidis—Perl package of functions and tools for manipulating microarray data and data files, contains ANOVA and T-test functions

	Array Finder
	Array Finder tool from Affymetrix—A simple web-based tool designed to find specific probe sets corresponding to genes on the GeneChip microarray platform

	ArrayViewer
	ArrayViewer from TIGR—A software tool designed to facilitate the presentation and analysis of microarray expression data, leading to the identification of genes that are differentially expressed; written in Java

	Array Pro
	Array Pro by Media Cybernetics—Array Pro Analyzer is an indispensable tool for the nascent microarray and high-throughput screening research efforts fueling the genomics, proteomics, drug discovery and bioinformatics revolution

	Array Vision
	Array Vision by Imaging Research—ArrayVision is a flexible software package that has been developed for the quantification of gene expression and protein arrays

	BASE
	BioArray Software Environment from Theoretical Physics group at Lunds University—BASE is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis

	Biodiscovery
	Biodiscovery, Inc.Homepage—Set of commercial software packages designed to analyze and manage microarray data from both cDNA and oligonucleotide microarrays

	BRB Array Tools
	BRB ArrayTools Homepage from the National Cancer Institute--BRB ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data; developed by statisticians experienced in the analysis of microarray data and involved in the development of improved methods for the design and analysis of microarray based experiments

	Centralizer
	Centralizer written by Alexander Zien—Centralizer is a program that computes normalization factors for gene expression data according to the centralization scheme

	CIT
	Cluster Identifcation Tool written by Kyle Furge—Discrimant cluster analysis of microarray gene expression data; Requires interaction with Eisens' Cluster and TreeView

	Clusfavor
	CLUSter and Factor Analysis with Varimax Orthogonal Rotation written by Leif Peterson—CLUSFAVOR is a Windows-based computer program for exploratory cluster and factor analysis. CLUSFAVOR was designed for large sample problems devoted to genomic analysis of gene expression data from cDNA and oligonucleotide microarrays

	Cluster
	Cluster written by Michael Eisen—Perform a variety of types of cluster analysis and other types of processing on large microarray datasets; Currently includes hierarchical clustering, self-organizing maps (SOMs), k-means clustering, principal component analysis; works in conjunction with Treeview

	CTWC Algorithm
	Coupled Two Way Clustering algorithm provided by the Weizmann Institute of Science—Register for free access to the CTWC algorithm and server to cluster expressional data

	Dapple
	Dapple written by Jeremy Buhler at the University of Washington—A Program for Analyzing cDNA Microarrays. Dapple is a tool for segmentation, spot-finding, and quantitation of cDNA microarrays. It implements various algorithms designed to make analysis of microarrays fast, accurate, and convenient for the user

	dCHIP
	DNA-Chip Analyzer from Harvard University—A free microarray analysis software package that utilizes an intensity modeling approach to microarray analysis

	Expression Profiler
	Expression Profiler from J. VIlo at EBI—Expression Profiler is a set of tools for clustering, analysis and visualization of gene expression and other genomic data

	F-Scan
	F-Scan from NIH—A free microarray analysis program from NIH for analysis of fluorescently probed cDNA arrays

	Freeview
	Freeview written by Marko Kavcic and Blaz Zupan—FreeView and FreeOView are programs for viewing and optimizing gene expression dendrograms

Gene Array Analyzer Software

GAAS created by MI Poli—GAAS is an integrated software framework for efficient management, analysis and visualization of large amounts of gene expression data across replicated experiments. It is structured in management, analysis and visualization sections that allow dealing with several gene expression dataset formats, custom differential expression data analyses, suitable visualization, and storage of results

	Geneclust
	Geneclust written by Paul Roebuck—GeneClust is a tool for exploratory analysis of gene expression microarray data featuring Hierarchical clustering and Gene shaving coupled with simulation to assess performance of the above methods. Needs S

	GeneCluster 2
	Clustering Software provided by the Whitehead Institute, Center for Genome Research—Freeware clustering tool that utilizes the weighted voting (WV) and k-nearest neighbor (KNN) algorithms to cluster expression data

	GeneDirector
	GeneDirector from BioDiscovery—GeneDirector helps you organize and manage all data generated across the entire array experimental process from array creation, sample preparation, hybridization, image analysis to data analysis

	GenePix Pro
	GenePix Pro from Axon Instruments—GenePix Pro is a software from Axon Instruments, Inc. for analyzing DNA and protein micrarrays, tissue arrays and cell arrays; images acquired from either Axon Scanner or third-party scanners can be used

	GeneSifter.net
	VizX Labs, Inc. Homepage—Commercial company and makers of GeneSifter, a web-based microarray data analysis software package, capable of comparison analyses from any microarray data; includes statistical tests, functional annotations, heat diagrams and scatter plots, and general data analysis tools

	Genesis
	Genesis from Graz University—A Java suite containing various tools such as filters, normalization, visualization tools, common clustering algorithms, SOM, k-means, PCA, SVM, map gene onto chromosomal sequences

	GeneSOM
	GeneSOM written by Jun Yan—R package for Clustering Genes using Self-Organizing Map

	GeneSpring
	GeneSpring from Silicon Genetics—GeneSpring is an all-inclusive software program widely regarded as the gold standard in expressional array analysis; includes clustering, statistical analysis, data filtering, and database integration

	GeNET
	GeNet from Silicon Genetics—GeNet is the most scalable and robust expression data management solution available, meeting the demands of both high-throughput sample volumes and increasing numbers of users

	GeneTraffic
	GeneTraffic from Iobion Informatics—GeneTraffic is offered in three convenient packages: one for Affymetrix GeneChip microarray data, one for standard two-color microarray data, and one that is a combination package allowing you to manage both types of formats

	GeneX-Lite
	GeneX-Lite from NCGR—GeneX-Lite is a client application that provides an interface to a relational database managment system (RDBMS)

	GESSES
	GESSES written by Joshua Deutsch—GESSES (genetic evolution of sub-spaces of expressed sequences); The algorithm computes an ensemble of predictors containing a minimal number of genes

	gp3
	GenePix Post-Processing Script from the Zacharewski Lab at Michigan State University—A Perl script that takes a GenePix results file and processes the raw data from it by performing signal filtering, background correction and signal normalization

	ISIS
	ISIS written by Anja von Heydebreck and Wolfgang Huber—ISIS is an R/C++ implementation of the class discovery method for gene expression data

	J-Express Pro
	J-Express Pro from Molmine—J-Express Pro is a comprehensive portable software package for analysis and visualisation of microarray data. The program gives access to multidimensional scaling, clustering, and visualisation in an integrated and flexible way. Its efficiency allows interactive clustering of thousands of expression profiles on standard personal computers

	KNNimpute
	KNNimpute distrubuted through Stanford University—KNNimputeis a program for estimating missing values for gene expression data

	Maanova
	Maanova from the Jackson Laboratory—MicroArray ANalysis Of VAriance (maanova) provides a complete work flow for microarray data analysis including: Data quality checks and visualization, data transformation, ANOVA model fitting for both fixed and mixed effects models, statistical tests including permutation, confidence interval with bootstrapping, cluster analysis; R add-on package

	Matrix2PNG
	Matrix2PNG written by Paul Pavlidis—Converts a gene expression matrix to an image in .png format

	MaxD
	MaxD from Manchester University—Maxd is a data warehouse and visualisation environment for genomic expression data

	Microarray Explorer
	Microarray Explorer (MAExplorer) software from the Laboratory of Experimental and Computational Biology at the National Cancer Institute— A free software package designed to analyze gene expression data from cDNA or oligonucleotide microarrays

	MicroArray Suite
	MicroArray Suite from Scanalytics—MicroArray Suite is Scanalytics image analysis software for visualizing and extracting data from DNA microarrays

	NetAFFX
	NetAFFX Analysis Center from Affmymetrix—A collection of analysis tools and database information related to the analysis of GeneChip data; includes annotations, NCBI links, sequence information, and a functional ontology tool(requires free registration)

	NOMAD
	Nomad from UCSF—NOMAD is an open source system for storing and querying the results of microarray experiments

PAGE

Patterns from Gene Expression from the University of Pennsylvania—PaGE is a tool to attach descriptive yet dependable, and easily interpretable expression patterns to genes represented in a collection of hybridization array experiments (macro- or micro-arrays); In particular, this incorporates a novel method to identify differentially expressed genes between two sample types with attached measures of confidence in the predictions made

	PAM
	Prediction Analysis for Microarrays from Stanford University—PAM does sample classification via nearest shrunken centroids, with many features including built-in cross-validation

	Pickgene
	Pickgene written by Brian Yandell—Functions to Analyze Microarray (Gene Expression) Data; currently available through BioConductor

	QT_Clust
	QT_Clust written by Witold Wolski—This is a reimplemantation of the QT_clust algorithm

	Rosetta Resolver
	Rosetta Resolver from Rosetta Biosoftware—The Rosetta Resolver system is a versatile and robust enterprise, gene expression data analysis system; also includes data management features

	SAM
	Significane of ANalysis of Microarrayswritten by R. Tibshirani—Supervised learning software for genomic expression data mining

	ScanAlyze
	cDNA array quantitation software written by Michael Eisen —Software for quatification of array signals from fluorescently labeled cDNA arrays

	SMA
	Statistical Microarray Analysis from UC, Berkeley—The package contains some simple functions for exploratory microarray analysis

	Spot
	Spot written by Jean Yang and Michael Buckley—Software for analysis of microarray images, built on top of Richard Beare's image analysis package, "Voir"

	Spotfire
	Spotfire, Inc. Hompage—Commercial software for data management and analysis of microarray data and functional genomic information

	SVDMAN
	SVDMAN written by Michael Wall and Patricia Dyck—Singular Value Decomposition Microarray Analysis is a program for singular value decomposition analysis of global gene expression data

	TM4
	TM4 Microarray Analaysis Packagee—A suite of microarray analysis software used primarily for cDNA micrarray analysis; includes software for spotfinding, quantification, and annotation

	tpWY
	tpWY from the University of Pennsylvania—This program computes t-statistics and p-values (both unadjusted and adjusted according to the Westfall and Young step-down algorithm) for two-sided alternative hypotheses

	Treeview
	Treeview written by Michael Eisen—Graphically browse results of clustering and other analyses from Cluster; Supports tree-based and image based browsing of hierarchical trees; works in conjunction with Cluster

	Vector Expression
	Vector Expression from Informax—Micrarray analysis suite using a friendly graphical interface and containing a complete set of peer-reviewed gene expression analysis tools

VERA and SAM

VERA and SAM maintained by Institute for Systems Biology and the WHitehead Institute—VERA - Variability and ERror Assessment: Estimates error model parameters from replicated, preprocessed experiments. SAM - Significance of Array Measurement: Uses error model to improve the accuracy of the expression ratio and to assign a value 'lambda' to each gene, indicating the likelihood that the gene is differentially expressed

	Xcluster
	Xcluster Clustering Software—Free clustering software created and hosted by Stanford University