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 |