Program name | Algorithm | Outputa | Missing datab | Assumptionsc | Key features | Limitations | Pool Size, MAX #Loci, Type | Platform | Ref.d |
---|---|---|---|---|---|---|---|---|---|
Pools2 | Clark's/EM | HF/HA | N/A | None | Haplotype-tagging SNPs | Computationally slow | Pools of 2 individuals, practical limit, biallelic | PC | [117] |
 |  |  |  |  | Accommodates a large number of SNPs | Need to re-calculate several times to assure consistent results |  |  |  |
 |  |  |  |  |  | EM issues |  |  |  |
LDPooled | EM | HF/HA | No | HWE | Calculates LD | LD impacts performance | Based on pools of 4 individuals, practical limit, biallelic | * | [96] |
 |  |  |  |  | SNPs or microsatellites | EM issues |  |  |  |
EHP.R | EM | HF | Yes | HWE | Tests haplotype-disease association | Variance increases with pool size, weaker LD and # loci | Pools of 4 individuals, practical limit, biallelic | PC/UNIX | [98] |
 |  |  |  |  | Assessment of haplotype frequency estimate accuracy | EM issues |  |  |  |
 |  |  |  |  | Handles different types of missing data | Requires knowledge of S-Plus 6.0 or R |  |  |  |