Computing hardwareStatistical Genetics Tools

ChromoPainter & fineSTRUCTURE

ChromoPainter is a package designed for finding and visualising haplotypes in sequence data.

fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data.                                                

URL: http://www.maths.bris.ac.uk/~madjl/finestructure/finestructure_info.html

Email: hellenth@stats.ox.ac.uk

Email: myers@stats.ox.ac.uk

Email: dan.lawson@bristol.ac.uk

ChromoPainterDeveloped by:

Dr Simon Myers

Dr Garrett Hellenthal

fineSTRUCTUREDr Daniel Lawson

Dr Daniel Falush

 

 

GREVE

The Genomic Recurrent Event ViEwer (GREVE) software tool creates genome wide or per chromosome plots and summaries of a user generated list of events, typically Copy Number Variations (CNVs), and genes.

URL: http://www.well.ox.ac.uk/GREVE/

Email: jcazier@well.ox.ac.uk

GREVEDeveloped by:

Dr Jean-Baptiste Cazier

 

 

GWAMA

GWAMA (Genome-Wide Association Meta Analysis)  is a software tool designed to perform meta-analysis of the results of Genome-wide association (GWA) studies of binary or quantitative phenotypes in order to identify signals of association. 

URL: http://www.well.ox.ac.uk/gwama/

Email: reedik@well.ox.ac.uk

Email: amorris@well.ox.ac.uk

GWAMADeveloped by:

Dr Reedik Magi

Dr Andrew Morris

 

 

Happy

HAPPY is designed to map Quantitative Trait Loci (QTL) in outbred populations descended from crosses between inbred lines.

URL: http://www.well.ox.ac.uk/happy/intro.shtml

Email: richard.mott@well.ox.ac.uk

HAPPYDeveloped by:

Prof Richard Mott

 

 

LDhat

LDhat is a package for analysing patterns of linkage disequilibrium and estimating recombination rates from population genetic data.

 URL: http://ldhat.sourceforge.net/

Email: adam.auton@einstein.yu.edu

LDhatDeveloped by:

Dr Adam Auton

Prof Gil McVean

 

 

Marchini Software

A suite of software tools written to facilitate the analysis of genome-wide association studies including IMPUTE and SNPTEST.

URL: http://www.stats.ox.ac.uk/~marchini/software/gwas/gwas.html

Email: marchini@stats.ox.ac.uk

Marchini SoftwareDeveloped by:

Dr Jonathon Marchini