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Software

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. For the conditions governing the use of Broad Institute software, please see the software use agreement associated with the tools you choose to download.

Use our search function, browse the complete software collection or click on one of the software categories listed below:

All   Chemical Biology     Image Analysis     Proteomics     Portals     Tool Suites    Visualization
Genetic Analysis:   GWAS   Genetic Variation   Linkage Analysis   Gene Expression
Sequence Analysis:   Assembly   Annotation   Alignment   RNAi   RNA-seq   Primer Design   Next Generation Tools   Phylogenetic Analysis   Gene Structure  Viral

  • GENE-E

    GENE-E is a matrix visualization and analysis platform designed to support visual data exploration. It includes heat map, clustering, filtering, charting, marker selection, and many other tools. In addition to supporting generic matrices, GENE-E also contains tools that are designed specifically for RNAi and gene expression data.

  • 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.

  • GeneHunter

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

  • GenePattern

    GenePattern is a powerful genomic analysis platform that provides access to more than 150 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research..

  • Genome Analysis Toolkit (GATK)

    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.

  • 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.

  • Heritability Calculator

    Heritability Calculator (HC) is a comprehensive package enabling the calculations of epidemiological and genetic parameters (such as broad/narrow sense heritabilities, true and population based heritability estimates, familial relative risk, marginal and epistatic effect size, detection power) for general (non-additive) genetic architectures.
     

  • ICBP Data & Analysis Portal

    The ICBP Data and Analysis Portal serves as an information hub of the ICBP program enabling resource sharing, annotation, and data integration and analysis. The portal provides access to datasets, analysis tools, visualizations, and other resources produced by the ICBP Centers for Cancer Systems Biology.

  • Inchworm

    Inchworm assembles the RNA-Seq data into the unique sequences of transcripts, often generating full-length transcripts for a dominant isoform, but then reports just the unique portions of alternatively spliced transcripts.