software

Software and Services

We develop and maintain a variety of software and web services.

PolyPhen-2 is a tool for predicting the effect of an amino acid substitution on protein structure and function, based on comparative genomics and experimentally determined protein structures. It is available as a web service, and can also be downloaded as a standalone application.
SNPtrack is a simple interface for mutation mapping and identifying causal mutations from whole-genome sequencing studies. It is available as a web service.
SCONE is a tool for predicting the effect of noncoding variation on regulatory sequences based on evolutionary conservation. It is available for download as a standalone application.
PINES (Phenotype-Informed Noncoding Element Scoring) evaluates the functional impact of noncoding variants by integrating diverse epigenetic annotations, utilizing genomic annotations most relevant to phenotypes of interest.

EagleEye is a tool for filtering noise and background proteins from LC-MS/MS spectra. It is available as a web service.
MS-BLAST is a tool for searching protein sequences identified with tandem mass spectrometry against databases of protein sequences. It is available as a web service.

Joint Likelihood Mapping (JLIM) is a tool to test for shared genetic effect between two genetic association data, for example, a disease GWAS study and gene expression QTL (eQTL) study.
Joint Likelihood Mapping 2 (JLIM_2.0) is a version of JLIM which supports meta-analysis across more than one cohort of matching ancestry.
Joint Likelihood Mapping (JLIM) 2.5 is a new version of JLIM based on summary statistics.
NPS is a tool for polygenic risk scoring based on partitioning-based non-parametric shrinkage algorithm.

CBaSE enables cancer type and gene-specific estimation of the strength of negative and positive selection. It is available as a browser-based tool as well as for download as a standalone package.

simDoSe is a fast and flexible Wright-Fisher simulator for arbitrary diploid selection evolving through realistic human demography.