~~REDIRECT>https://sunyaevlab.hms.harvard.edu/wiki/!web/software~~
=====Software and Services=====

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

===Tools for Assessment of Variants===
  * [[http://genetics.bwh.harvard.edu/pph2/|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.
  * [[http://genetics.bwh.harvard.edu/snptrack|SNPtrack]] is a simple interface for mutation mapping and identifying causal mutations from whole-genome sequencing studies. It is available as a web service.
  * [[http://genetics.bwh.harvard.edu/scone/|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.
  * [[http://genetics.bwh.harvard.edu/pines/|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.

===Tools for Mass Spectrometry and Proteomics===
  * [[http://genetics.bwh.harvard.edu/cgi-bin/msfilter/eagleeye.cgi|EagleEye]] is a tool for filtering noise and background proteins from LC-MS/MS spectra. It is available as a web service.
  * [[http://genetics.bwh.harvard.edu/msblast|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.

===Tools for Statistical Genetics===
  * [[ 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. 
  * [[ JLIM2.0 ]] is a version of JLIM which supports meta-analysis across more than one cohort of matching ancestry. 
  * [[ JLIM2.5 ]] is a new version of JLIM based on summary statistics.
  * [[ http://github.com/sgchun/nps|NPS ]] is a tool for polygenic risk scoring based on partitioning-based non-parametric shrinkage algorithm.

===Tools for Cancer Genomics===
  * [[ http://genetics.bwh.harvard.edu/cbase/index.html|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.

===Tools for Population Genetics===
  * [[https://github.com/dbalick/simDoSe|simDoSe]] is a fast and flexible Wright-Fisher simulator for arbitrary diploid selection evolving through realistic human demography.