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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

  • ALLPATHS

    ALLPATHS is a whole genome shotgun assembler that can generate high quality assemblies from short reads.

  • AmosCmp16Spipeline

    AmosCmp16Spipeline uses the AMOScmp software to assemble multiple, potentially overlapping 16S rRNA sequencing reads based on read mappings to a reference 16S rRNA gene.

  • Arachne

    Arachne is a tool for assembling genome sequences from whole genome shotgun reads, mostly in forward-reverse pairs obtained by sequencing clone ends.

  • Argo

    The Argo Genome Browser is a production tool for visualizing and manually annotating whole genomes.

  • ChimeraSlayer

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

  • 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.

  • GENE-E

    GENE-E is a matrix visualization and analysis platform designed to support visual data exploration. It includes heat map, clustering, filtering, charting, marker selection, and many other tools. In addition to supporting generic matrices, GENE-E also contains tools that are designed specifically for RNAi and gene expression 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.

  • 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.

  • NAST-iEr

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