Scientists in the Broad community have developed many critical software tools for the analysis of increasingly large genome-related datasets, and they make these tools openly available to the scientific community (see below).
For the conditions governing the use of Broad Institute software, please see the software use agreement associated with the tools you choose to download.
Integrative Genomics Viewer
Integrative Genomics Viewer
The Integrative Genomics Viewer (IGV) is a visualization tool to simultaneously integrate and analyze multiple types of genomic data.
Genetic analysis
Birdsuite
The Birdsuite is a fully open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform.
Genome Analysis Toolkit
The Genome Analysis Toolkit (GATK) is a structured programming framework designed to enable the rapid development of efficient and robust analysis tools for next-generation DNA sequencers. The GATK solves the data management challenge by separating data access patterns from analysis algorithms, using the functional programming philosophy of Map/Reduce. Since the GATK’s traversal engine encapsulates the complexity of efficiently accessing the next-generation sequencing data, researchers and developers are free to focus on their specific analysis algorithms. This not only vastly improves the productivity of developers, who can quickly write new analyses, but also results in tools that are efficient and robust, and can benefit from improvements to a common data management engine.
Ultrasome
Ultrasome is an extremely efficient methodology for detecting gains and losses of chromosomal material in DNA copy-number data. The program processes latest-generation copy number arrays about 10,000 times faster than standard methods (e.g., CBS) while retaining comparable analyticaccuracy.
Genome sequence
ALLPATHS
ALLPATHS is a whole genome shotgun assembler that can generate high quality assemblies from short reads.
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.
Medea
Medea is a suite of Adobe® Flash® based comparative genomic visualization tools including a Circular Genome Viewer, parallel Genome Map, Synteny Map, Dot Plot, and Viral Viewer.
PriSM
PriSM is a set of algorithms designed specifically to create degenerate primers for the amplification and sequencing of short viral genomes while maintaining sample population diversity.
Siphy
Siphy analyzes multiple sequence alignments and single outs bases or small regions that are undergoing selection by looking at reduction in substitution rates and unexpected detecting substitution patterns. A specific program to detect conserved transcription factor binding sites is also available.
Spines
Spines is a C++ software package for genomic sequence alignment and analysis. The source code is publicly available under the Gnu Lesser General Public License .
SWAP454
SWAP454 is a tool for calling SNPs using 454 read data.
VAAL
VAAL is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants.
Genetic variation
EIGENSTRAT
EIGENSTRAT detects and corrects for population stratification in genome-wide association studies using principal components analysis.
GRAIL
GRAIL is an algorithm to assess biological relationships between disease-associated genetic variants.
Haploview
Haploview is designed to facilitate the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.
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.
SNAP
SNAP is a web server for finding and annotating proxy SNPs based on linkage disequilibrium, genomic location, and coverage by commercial genotyping arrays.
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. GenePattern is available for MacOS, Windows, and Linux platforms.
Gene Set Enrichment Analysis
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.
Chemical Biology
ChemBank
ChemBank is the flagship project of the Chemical Biology Program and Platform, incorporating small-molecule structure and screening data from the Broad Institute's high-throughput screening facilities.
SpectralNET
SpectralNET is a tool to analyze networks of interactions, such as chemical-genetic networks [see also Haggarty (2003) , Forman (2005) ]. It is available as a standalone Windows application and as a web-enabled version.
Other
Primer3
Primer3 is a tool used to choose primers for PCR reactions.
