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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:

All   Chemical Biology     Image Analysis     Proteomics     Portals     Tool Suites    Visualization
Genetic Analysis:   GWAS   Genetic Variation   Linkage Analysis   Gene Expression
Sequence Analysis:   Assembly   Annotation   Alignment   RNAi   RNA-seq   Primer Design   Next Generation Tools   Phylogenetic Analysis   Gene Structure  Viral

  • 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.

  • InVEx

    InVEx (Introns Vs Exons) is a permutation-based method (written in Python) for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations. The method was developed for use in cancer genomics studies, with particular relevance to high mutation rate cancers. Mutations are permuted on a per-patient, per-trinucleotide-context basis across the exons, introns and UTRs of a gene, generating a null model of the distribution of mutations to which the observed distribution can be compared to determine statistical significance. Significant genes are of interest, as their somatic mutation is likely to be important in the formation of the cancer being studied. The method can operate on whole exome as well as whole genome sequencing data.

  • Kinannote

    Kinannote identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine/threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. If the user inputs a complete proteome, additional modules are available to evaluate the completeness of the kinome and place it in context with reference kinomes.

  • Locusview

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

  • MAGENTA

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

  • 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.

  • 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.