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Table 3 Haplotyping software for hypothesis testing and analysis.

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

Program name Haplotyping algorithm Key analysis feature(s) Discrete outcomea Continuous outcomeb
Hypothesis     
CHAPLIN ECM Includes likelihood ratio statistic and score statistic for haplotype-phenotype analysis, uses permutation test to determine significance Yes, case-control No
   Includes AIC for model selection, does not accommodate covariates   
EH EM Test for LD for unrelated and in case-control Yes, case-control No
   Test for frequency difference between case-control under: H1 association, H2 association for all loci   
EHPLUS EM Improves on EH Yes, case-control No
   Model-free analysis and permutation test   
FASTEHPLUS EM Implements EH and EHPLUS test Yes, case-control No
   Significant speed improvements   
GENECOUNTING EM Compares overall and specific haplotype frequency between cases and controls Yes, case-control No
HAPH IP Phylogeny based haplotyping method Yes, case-control Yes
   Uses information from phylogeny for analysis, includes parametric and non-parametric tests for qualitative and quantitative phenotypes   
HAPLO.STATS EM Score statistic for haplotype-phenotype analysis Yes, binary, ordinal, & Poisson Yes
   GLM for regression of trait on haplotype, adjustment for covariates and interaction   
HPLUS EE +PL+ EM Compares haplotypes frequency between cases and controls, option to adjust for covariates, and interaction assessment Yes, case-control No
   Reports OR, confidence interval and identifies haplotype blocks   
LDSUPPORT EM Uses likelihood method to calculate risk of developing disease phenotype from diplotype configuration Yes, case-control No
PHASE v2.0 MCMC Allows comparison of haplotype frequency between populations Yes, case-control No
THESIAS S-EM Compares haplotypes frequency between cases and controls, survival analysis, option to adjust for covariates and interaction assessment Yes, case-control, survival analysis Yes
   Uses Chi-square statistics/t-test for analysis   
SAS Genetics EM Allows comparison of haplotype frequency between populations Yes, case-control Yes
   Haplotype trend regression (HTR) and several population genetic tests   
   TDT test for family data   
SNPEM EM Compares overall and specific haplotype frequency between cases and controls Yes, case-control No
   Includes batch feature for sliding windows analysis   
WHAP EM Uses SNPHAP for regression based haplotype association test on SNPs, provides beta estimates of effects Yes, case-control Yes
   Includes haplotype weighted likelihood analysis, permutation tests and sliding windows analysis   
Zaykin et al. EM Likelihood ratio statistic for haplotype-phenotype analysis Yes, case-control Yes
   Allows sliding windows analysis   
3locus.PAS EM Test for global disequilibrium, including pairwise and three No No
   way disequilibrium for an unrelated sample   
Other analysis programs     
Arlequin v2.0/3.0 EM/ELB Several population genetic tests   
Zou and Zhao EM Adjust haplotype frequency estimates for genotyping error   
  1. a Qualitative phenotype.
  2. b Quantitative phenotype.
  3. AIC: Akaike's Information Criterion; EE: Estimating equation; ELB: Excoffier-Laval-Balding algorithm, Bayesian; ECM: Expectation Conditional maximisation algorithm; EM: Expectation maximisation algorithm; GLM: General Linear Model; IP: Imperfect phylogeny; MCMC: Markov Chain Monte Carlo algorithm, Bayesian algorithm; OR: Odds Ratio; PL: Partition ligation algorithm; S-EM: Stochastic EM algorithm.