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:

  • MapMaker3

    MapMaker is a package containing a program for genetic linkage analysis and a program for mapping genes underlying complex traits.

  • MEDEA

    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.

  • Medulloblastoma Portal

    A collection of recent publications aimed at identifying the drivers of medulloblastoma, such as mutations or chromosome alterations, which will enable development of more effective and and less toxic targeted therapies.

  • Multiple Myeloma Genomics Portal (MMGP)

    The Multiple Myeloma Genomics Portal (MMGP) provides access to and analysis of the MMGP portal data sets. These include the MMRC-funded reference collection of paired aCGH and gene expression data as well as several additional public multiple myeloma datasets.

  • NAST-iEr

    The NAST-iEr alignment utility aligns a single raw nucleotide sequence against one or more NAST formatted sequences.

  • NMF (Non-negative Matrix Factorization)

    NMF (Non-negative Matrix Factorization), an algorithm based on decomposition-by-parts, recovers meaningful information without supervision. Coupled with a novel model selection mechanism, and efficiently implemented in Matlab, NMF is a powerful method for identification of context-dependent patterns in complex biological systems.

  • Nozzle

    Nozzle is an R package for generation of reports in high-throughput data analysis pipelines. Nozzle reports are implemented in HTML, JavaScript, and Cascading Style Sheets (CSS), but developers do not need any knowledge of these technologies to work with Nozzle. Instead they can use a simple R API to design and implement powerful reports with advanced features such as foldable sections, zoomable figures, sortable tables, and supplementary information.

    Please cite our Bioinformatics paper if you are using Nozzle in your work.

  • 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.

  • PLINK

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

  • Primer3

    Primer3 is a tool used to choose primers for PCR reactions.