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:

  • Argo

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

  • Broad-Novartis Cancer Cell Line Encyclopedia (CCLE)

    The Cancer Cell Line Encyclopedia (CCLE) project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access analysis and visualization of DNA copy number, mRNA expression and mutation data for about 1000 cell lines. 

  • 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.

  • GenomeSpace

    GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface. GenomeSpace provides access to a diverse range of bioinformatics tools, and bridges the gaps between the tools, making it easy to leverage the available analyses and visualizations in each of them. The tools retain their native look and feel, with GenomeSpace providing frictionless conduits between them through a lightweight interoperability layer. GenomeSpace does not perform any analyses itself; these are done within the member tools wherever they live – desktop, Web service, cloud, in-house server, etc. Rather, GenomeSpace provides tool selection and launch capabilities, and acts as a data highway automatically reformatting data as required when results move from the output of one tool to input for the next.

  • Haploview

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

  • 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.

  • Integrative Genomics Portal (IGP)

    The Broad Integrative Genomics Portal allows the sharing (both private and public) of annotated and integrated genomic datasets. Funded by the Starr consortium, the portal provides both data analyses and visualizations.

  • Integrative Genomics Viewer

    The Integrative Genomics Viewer (IGV) is a visualization tool to simultaneously integrate and analyze multiple types of genomic data.

  • Locusview

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


    MEDEA is a suite of Adobe® Flash® based comparative genomic visualization tools including a Circular Genome Viewer, parallel Genome Map, Synteny Map, and Dot Plot.