Software

Genome Sequence

Arachne
Arachne is a tool for assembling genome sequences from whole genome shotgun reads, mostly in forward-reverse pairs obtained by sequencing clone ends.

Argo
The Argo Genome Browser is a production tool for visualizing and manually annotating whole genomes.

Conrad
The Conrad gene caller is tool for predicting gene structures in DNA based on the DNA sequence and other available evidence. >Support

Genetic Variation

EIGENSTRAT
detects and corrects for population stratification in genome-wide association studies using principal components analysis. >Support

Haploview
Haploview is designed to facilitate the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. >Support

Locusview
LocusView is a program for generating images of chromosomal regions annotated with genomic features, experimental data and analysis results.

PLINK
PLINK is a comprehensive toolset for statistical analysis in whole-genome association studies

Sweep
Sweep allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection.

Tagger
Tagger is a web server for the selection and evaluation of tag SNPs from genotype data.

Linkage Analysis

GeneHunter
GeneHunter is a tool for rapid extraction of complete multipoint linkage analysis using both parametric and nonparametric approaches.

MapMaker3
MapMaker is a package containing a program for genetic linkage analysis and a program for mapping genes underlying complex traits.

High-throughput image analysis

CellProfiler
CellProfiler cell image analysis software quantitatively measures phenotypes from thousands of images automatically, usually for high throughput image based cell screening experiments.

CellProfiler Analyst
CellProfiler Analyst data exploration and analysis software is designed for complex and interactive exploration of multidimensional data, specifically from high-throughput image-based experiments.

Expression Analysis

GenePattern
GenePattern is a software package for the analysis of molecular profiles, e.g., genome-wide microarray expression signatures. It includes a collection of analytic and visualization tools, interfaces for the easy construction of analytic pipelines and integration of new modules without additional programming. Gene Pattern is available for MacOS, Windows, and Linux platforms.

Gene Set Enrichment Analysis (GSEA)
GSEA is a computational method that determines if a given set of genes shows statistically significant differences between two biological states. It is useful for interpreting the results of gene expression studies.

GeneCruiser
GeneCruiser is an annotation tool that allows users to map genes from genomic databases to Affymetrix probes, find information about Affymetrix probes in genomic databases and find where Affymetrix probes are located in the human genome.

Connectivity Map
The Connectivity Map is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of decisive functional connections between drugs, genes, and diseases. This web interface is designed to allow biologists, pharmacologists, chemists and clinical scientists to use our analysis tools, and access the raw data.

Other

Primer3
Primer3 is a tool used to choose primers for PCR reactions.

RHMapper
RHMapper is a web-based Program that allows researchers to map STSs relative to the radiation hybrid map of the human genome.

FTP Software Archive (prior to 2001)

Software Documentation (prior to 2001)