CHAPLIN

ECM

Includes likelihood ratio statistic and score statistic for haplotypephenotype analysis, uses permutation test to determine significance

Yes, casecontrol

No

 
Includes AIC for model selection, does not accommodate covariates
  
EH

EM

Test for LD for unrelated and in casecontrol

Yes, casecontrol

No

 
Test for frequency difference between casecontrol under: H1 association, H2 association for all loci
  
EHPLUS

EM

Improves on EH

Yes, casecontrol

No

 
Modelfree analysis and permutation test
  
FASTEHPLUS

EM

Implements EH and EHPLUS test

Yes, casecontrol

No

 
Significant speed improvements
  
GENECOUNTING

EM

Compares overall and specific haplotype frequency between cases and controls

Yes, casecontrol

No

HAP^{H}

IP

Phylogeny based haplotyping method

Yes, casecontrol

Yes

 
Uses information from phylogeny for analysis, includes parametric and nonparametric tests for qualitative and quantitative phenotypes
  
HAPLO.STATS

EM

Score statistic for haplotypephenotype 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, casecontrol

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, casecontrol

No

PHASE v2.0

MCMC

Allows comparison of haplotype frequency between populations

Yes, casecontrol

No

THESIAS

SEM

Compares haplotypes frequency between cases and controls, survival
analysis, option to adjust for covariates and interaction assessment

Yes, casecontrol,
survival analysis

Yes

 
Uses Chisquare statistics/ttest for analysis
  
SAS Genetics

EM

Allows comparison of haplotype frequency between populations

Yes, casecontrol

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, casecontrol

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, casecontrol

Yes

 
Includes haplotype weighted likelihood analysis, permutation
tests and sliding windows analysis
  
Zaykin et al.

EM

Likelihood ratio statistic for haplotypephenotype analysis

Yes, casecontrol

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
  