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:


    PLINK is a comprehensive toolset for statistical analysis in whole-genome association studies.

  • SNAP

    SNAP is a web server for finding and annotating proxy SNPs based on linkage disequilibrium, genomic location, and coverage by commercial genotyping arrays.

  • Sweep

    Sweep allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection.

  • Tagger

    Tagger is a web server for the selection and evaluation of tag SNPs from genotype data.

  • TreeChopper

    TreeChopper clusters tree leaf nodes according to phylogenetic distance.

  • 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.