Data Tools and Resources

ampliconDIVider
ampliconDIVider identifies deletion and insertion variants (DIVs) in DNA amplicons.

bam2mpg
A Bayesian genotype caller for NextGen sequencing data.

BuddySuite
A collection of four independent, yet interrelated, command line programs that facilitate each step in the workflow of sequence discovery, curation, alignment, and phylogenetic reconstruction.

Complementary Pairs Stability Selection for Genome-Wide Association Studies (ComPaSS-GWAS)
An ad-hoc alternative to replication that can reduce type I errors for GWA studies when appropriate replication data are not available.

Conserved Domain-based Prediction (CDPred)
A computational algorithm that is designed to theoretically calculate the effect of substituting an amino acid relative to the reference sequence within functional modules - the protein domains.

GeIST
A set of files and scripts used to detect and annotate MLV integration sites.

GeneLink
A data management system designed to facilitate genetic studies of complex traits.

Genometric Analysis Simulation Program (G.A.S.P.)
A software tool that can generate samples of family data based on user specified genetic models.

r2VIM
A new recurrency-based variable selection method in random forests for genome-wide genetic association studies.

ROMPrev
A software suite for quantitative trait and locus-specific heritability estimation and association testing using the revised ROMP method.

Shimmer
A tool for the detection of genetic alterations in tumors from Next Generation sequence data.

SKIPPY
A tool for scoring exonic variants for features associated with exon skipping and ectopic splice site creation.

SOOP
A tool for the design and selection of overgo probes optimized for high-throughput comparative mapping.

SubmiRine
A software package for predicting microRNA target site variants (miR-TSVs) from clinical genomic data sets.

Tiled Regression Analysis
A software framework for selecting a set of genetic predictors which jointly and independently explain trait variation with an additive regression model.

trieFinder
A tool that rapidly maps sequence tags to RefSeq, UniGene, and genomic sequences, providing output amenable to both transcript quantification and the detection of novel transcripts.

Var-MD
An annotation and analysis tool for next-generation sequencing variants in rare diseases and small pedigrees.

VarSifter
VarSifter is a graphical java program designed to display, sort, filter, and generally sift variation data from massively parallel sequencing experiments.