Computational Methods

Garrett Hellenthal Group
 

ChromoPainterv2: inferring haplotype sharing among individuals  

Download Software

Paper: Inference of Population Structure using Dense Haplotype Data

fineSTRUCTURE: clustering individuals based on haplotype sharing 

Download Software

Paper: Inference of Population Structure using Dense Haplotype Data

SOURCEFIND: inferring proportions of recent ancestry sharing among individuals/groups 

Download Software

Paper: Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance

GLOBETROTTER: identifying/dating/describing admixture events in a target population 

Download Software

Paper: A Genetic Atlas of Human Admixture History

Dave Curtis Group

Software and scripts to analyse relationship between genetic variants and complex disease phenotypes, especially utilising sequence data

Richard Mott Group

Genotype Encryption
 

• Download Software
   
• Paper: Private Genomes and Public SNPs: Homomorphic Encryption of Genotypes and Phenotypes for Shared Quantitative Genetics
   
• Try to crack the encryption and win $1000

Imputation methods for low coverage sequencing
 

• Haplotype mosaic reconstruction for MAGIC populations
   
• See also STITCH (lead: Robert W Davies, Oxford)

Software for Analysing Multiparental populations 

• HAPPY software for QTL mapping

Genotypes and Phenotypes for Arabidopsis and Wheat MAGIC populations

• Download Software