Table 4.
Description of programs designed for pooled samples.
| 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 |
a Program haplotype output, individual assignment, frequency estimates or both.
b Ability of program to accept missing data.
c Program assumptions.
d List of references.
*Could not determine from available data.
EM: Expectation maximisation algorithm; EM issues: May be sensitive to HWE departures, long run times, and non-global max (requiring multiple restarts); HF: Haplotype frequency estimate; HA: Individual haplotype assignment; HWE: Hardy-Weinberg equilibrium; LD: Linkage disequilibrium; PC: IBM compatible personal computer; UNIX: Runs on Unix operating system, including Linux, FORTRAN, Solaris and others.