Reconstruction d'haplotypes¶

Software for inferring haplotype phase and missing genotype data and clustering of haplotypes¶

To cluster haplotypes and to perform association analysis Hapminer (Li et al., 2006): http://vorlon.case.edu/~jxl175/HapMiner.html
To infer haplotype phase and missing genotypes ! fastPHASE (Scheet and Stephens, 2006) [http://stephenslab.uchicago.edu/software.html
To infer haplotype phase and missing genotypes and to perform association analysis Beagle (Browning and Browning, 2007): http://faculty.washington.edu/browning/beagle/beagle.html
To infer missing genotypes : IMPUTE (Marchini et al., 2007): http://mathgen.stats.ox.ac.uk/impute/impute.html
To perform imputation-based Bayesian regression analysis ! BIM-BAM (Servin and Stephens, 2007): http://stephenslab.uchicago.edu/software.html
To find haplotypes and impute genotypes using multiple chip sets : findhap.f90 (Van Raden, 2010): http://aipl.arsusda.gov/software/findhap/
To infer and impute haplotypes : alphaPhase (Hickey et al., 2011): http://sites.google.com/site/hickeyjohn/alphaphase