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Table 2 Web-based haplotyping programs and related websites.

From: A comprehensive literature review of haplotyping software and methods for use with unrelated individuals

Haplotyping program Website Comments
GS-EM http://episun7.med.utah.edu/~alun/software.html Assigns probability to genotype calls
   Constructs haplotypes using probabilities
HAPH http://www.calit2.net/compbio/hap/ Imperfect phylogeny method
   Handles missing data
OSLEM http://genome3.cpmc.columbia.edu/~genome/HDL/ Modified EM algorithm that runs faster
   No missing data
PHASE v2.02 http://archimedes.well.ox.ac.uk/pise/ MCMC method
   Comparison HF between groups
   Handles missing data and recombination
SNPEM http://polymorphism.ucsd.edu/snpem/ EM method
   Comparison HF between groups
SNPHAP http://archimedes.well.ox.ac.uk/pise/ EM method
   Handles missing data
Haplotyping-related websites   
Boas Center for Genomics and Human Genetics: North Shore LIJ Research Institute http://www.nslij-genetics.org/soft/ Comprehensive list of statistical genetics software
   Mirrored by Rockefeller site
International HapMap Project http://www.hapmap.org HapMap project news, data and information
Laboratory of Statistical Genetics at Rockefeller University http://linkage.rockefeller.edu/soft/ Comprehensive list of statistical genetics software
   Mirror of North Shore LIJ site
MRC Rosalind Franklin Centre for Genomics Research http://www.hgmp.mrc.ac.uk/Registered/Menu/alphabet.html Registration required
   Numerous programs available
Power for Association with Errors http://linkage.rockefeller.edu/pawe/ Calculates power and sample size in the presence of differing genotype error rates
PRL: Polymorphism Research Lab http://polymorphism.ucsd.edu/ Additional information and links to all reviewed programs
The Wellcome Trust Centre for Human Genetics http://archimedes.well.ox.ac.uk/pise/ Several additional programs with links to their sources
  1. EM: Expectation maximisation algorithm; HF: Haplotype frequency estimate; MCMC: Markov Chain Monte Carlo algorithm, Bayesian.