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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
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
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.
AssembleViral454
AssembleViral454 is a new assembler, based on the ARACHNE package, designed for small and non repetitive genomes sequenced at high depth. Reads need not be paired, and it is assumed that no sequence repeat in the genome would be large enough to fully contain an average read.
The assembly process consists of two steps: First, a pre-processing stage is run, the output of which is an initial read layout. This is identical to the process employed in the published ARACHNE algorithm. This stage generally results in a fragmented assembly. Second, we employ an iterative procedure that incrementally merges contigs and improves read placement.
AssembleViral454 is implemented as a module of Arachne.
Birdsuite
The Birdsuite is a fully open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform.
Butterfly
Butterfly then processes the individual graphs in parallel, tracing the paths that reads and pairs of reads take within the graph, ultimately reporting full-length transcripts for alternatively spliced isoforms, and teasing apart transcripts that corresponds to paralogous genes.
Cancer Portals
A number of cancer portals have been developed to streamline viewing and analysis of related data.
CellProfiler
CellProfiler cell image analysis software quantitatively measures phenotypes from thousands of images automatically, usually for high-throughput image-based cell screening experiments.
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.