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:

  • NAST-iEr

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

  • Primer3

    Primer3 is a tool used to choose primers for PCR reactions.

  • PriSM

    PriSM is a set of algorithms designed specifically to create degenerate primers for the amplification and sequencing of short viral genomes while maintaining sample population diversity.

  • Scripture

    Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio.

  • Siphy

    Siphy analyzes multiple sequence alignments and single outs bases or small regions that are undergoing selection by looking at reduction in substitution rates and unexpected detecting substitution patterns. A specific program to detect conserved transcription factor binding sites is also available.

  • Spines

    Spines is a C++ software package for genomic sequence alignment and analysis. The source code is publicly available under the Gnu Lesser General Public License.

  • TreeChopper

    TreeChopper clusters tree leaf nodes according to phylogenetic distance.

  • WigeoN

    WigeoN examines the sequence conservation between a query and a trusted reference sequence