Table 2.
Web-based haplotyping programs and related websites.
| 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 |
EM: Expectation maximisation algorithm; HF: Haplotype frequency estimate; MCMC: Markov Chain Monte Carlo algorithm, Bayesian.