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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
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
PLINK
PLINK is a comprehensive toolset for statistical analysis in whole-genome association studies.
SNAP
SNAP is a web server for finding and annotating proxy SNPs based on linkage disequilibrium, genomic location, and coverage by commercial genotyping arrays.
Sweep
Sweep allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection.
Tagger
Tagger is a web server for the selection and evaluation of tag SNPs from genotype data.
TreeChopper
TreeChopper clusters tree leaf nodes according to phylogenetic distance.
Ultrasome
Ultrasome is an extremely efficient methodology for detecting gains and losses of chromosomal material in DNA copy-number data. The program processes latest-generation copy number arrays about 10,000 times faster than standard methods (e.g., CBS) while retaining comparable analyticaccuracy.
