Program name | Haplotyping algorithm | Key analysis feature(s) | Discrete outcome^{a} | Continuous outcome^{b} |
---|---|---|---|---|
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 |
HAP^{H} | 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 |