Table 2 Web-based haplotyping programs and related websites.

GS-EM

http://episun7.med.utah.edu/~alun/software.html

Assigns probability to genotype calls

Constructs haplotypes using probabilities

HAP^H

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