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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

  • CellProfiler Analyst

    CellProfiler Analyst data exploration and analysis software is designed for complex and interactive exploration of multidimensional data, specifically from high-throughput image-based experiments.

  • ChemBank

    ChemBank is the flagship project of the Chemical Biology Program and Platform, incorporating small-molecule structure and screening data from the Broad Institute's high-throughput screening facilities.

  • ChimeraSlayer

    ChimeraSlayer is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).

  • Chrysalis

    Chrysalis clusters the Inchworm contigs into clusters and constructs complete de Bruijn graphs for each cluster. Each cluster represents the full transcriptonal complexity for a given gene (or sets of genes that share sequences in common). Chrysalis then partitions the full read set among these disjoint graphs.

  • ComSeq

    ComSeq is a tool for designing and analyzing combinatorial pooling experiments for next-generation sequencing projects using compressed sensing technology. ComSeq enables the identification of novel rare alleles, as well as detection of individuals who are carriers of known SNPs in a large population in an efficient manner.

  • Connectivity Map

    The Connectivity Map is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of decisive functional connections between drugs, genes, and diseases. This web interface is designed to allow biologists, pharmacologists, chemists, and clinical scientists to use our analysis tools and access the raw data.

  • Differentiation Map Portal (DMAP)

    The Differentiation Map Portal (DMAP) contains data and publications used in the study of a differentiation map of hematopoiesis.

  • EIGENSTRAT

    EIGENSTRAT detects and corrects for population stratification in genome-wide association studies using principal components analysis.

  • Exome Enrichment Automation

    Automation of the Illumina TruSeq Exome Enrichment protocol on an Agilent Bravo liquid handling platform.

  • Gene Set Enrichment Analysis

    GSEA is a computational method that determines if a given set of genes shows statistically significant differences between two biological states. It is useful for interpreting the results of gene expression studies.