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:

  • Haploview

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

  • Heritability Calculator

    Heritability Calculator (HC) is a comprehensive package enabling the calculations of epidemiological and genetic parameters (such as broad/narrow sense heritabilities, true and population based heritability estimates, familial relative risk, marginal and epistatic effect size, detection power) for general (non-additive) genetic architectures.
     

  • 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.

  • Inchworm

    Inchworm assembles the RNA-Seq data into the unique sequences of transcripts, often generating full-length transcripts for a dominant isoform, but then reports just the unique portions of alternatively spliced transcripts.

  • 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.