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http://www.broadinstitute.org/genome_bio/siphy/
Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions.
Proper citation: SiPhy (RRID:SCR_000564) Copy
http://www.broadinstitute.org/cancer/cga/contest
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data.
Proper citation: ContEst (RRID:SCR_000595) Copy
https://software.broadinstitute.org/morpheus/
Software tool for versatile matrix visualization and analysis. Program to generate heatmaps from input data. JavaScript matrix visualization and analysis.
Proper citation: Morpheus by Broad Institute (RRID:SCR_017386) Copy
http://www.broad.mit.edu/cancer/software/genecluster2/gc2.html
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A software package for analyzing gene expression and other bioarray data, giving users a variety of methods to build and evaluate class predictors, visualize marker lists, cluster data and validate results. GeneCluster 2.0 greatly expands the data analysis capabilities of GeneCluster 1.0 by adding supervised classification, gene selection, class discovery and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting (WV) and k-nearest neighbor (KNN) algorithms, a module for systematically finding and evaluating clustering via self-organizing maps, and modules for marker gene selection and heat map visualization that allow users to view and sort samples and genes by many criteria. It enhances the clustering capabilities of GeneCluster 1.0 by adding a module for batch SOM clustering, and also includes a marker gene finder based on a KNN analysis and a visualization module. GeneCluster 2.0 is a stand-alone Java application and runs on any platform that supports the Java Runtime Environment version 1.3.1 or greater.
Proper citation: GeneCluster 2: An Advanced Toolset for Bioarray Analysis (RRID:SCR_008446) Copy
A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site.
Proper citation: Haploview (RRID:SCR_003076) Copy
http://www.broadinstitute.org/cancer/cga/rna-seqc
Java software which computes a series of quality control metrics for RNA-seq data and can compare sequencing quality across different samples or experiments to evaluate different experimental parameters. The input can be one or more BAM files, and the output consists of HTML reports and tab delimited files of metrics data.
Proper citation: RNA-SeQC (RRID:SCR_005120) Copy
Ratings or validation data are available for this resource
http://broadinstitute.github.io/picard/
Java toolset for working with next generation sequencing data in the BAM format.
Proper citation: Picard (RRID:SCR_006525) Copy
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