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:

  • 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.

  • 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.

  • ChimeraSlayer

    ChimeraSlayer is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).

  • Chrysalis

    Chrysalis clusters the Inchworm contigs into clusters and constructs complete de Bruijn graphs for each cluster. Each cluster represents the full transcriptonal complexity for a given gene (or sets of genes that share sequences in common). Chrysalis then partitions the full read set among these disjoint graphs.

  • ComSeq

    ComSeq is a tool for designing and analyzing combinatorial pooling experiments for next-generation sequencing projects using compressed sensing technology. ComSeq enables the identification of novel rare alleles, as well as detection of individuals who are carriers of known SNPs in a large population in an efficient manner.

  • 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.

  • Differentiation Map Portal (DMAP)

    The Differentiation Map Portal (DMAP) contains data and publications used in the study of a differentiation map of hematopoiesis.


    DISCOVAR is a variant caller and genome assembler that uses the latest low cost sequencing data. It can generate highly accurate variant calls for individual humans, or assemble genomes de novo.

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