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:


    HLA typing from exome capture sequencing.

  • GenePattern

    GenePattern is a powerful genomic analysis platform that provides access to hundreds of 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..

  • 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.


    MAGENTA is a program that tests whether predefined biological processes or gene sets are enriched for genes associated with a complex disease or trait.

  • Pilon

    Pilon uses read alignment analysis to diagnose, report, and automatically improve genome assemblies, and it can also be used to make variant calls among similar haploid strains.

  • 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.

  • V-Phaser

    V-Phaser is a tool to call variants in mixed populations from ultra-deep sequence data. V-Phaser combines information regarding the covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity. V-Phaser can reliably detect rare variants in mixed populations that occur at frequencies of <1%. The V-Phaser package also includes V-Profiler a tool to analyze and visualize variants.