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Table 4 Description of programs designed for pooled samples.

From: A comprehensive literature review of haplotyping software and methods for use with unrelated individuals

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 		   
  1. a Program haplotype output, individual assignment, frequency estimates or both.
  2. b Ability of program to accept missing data.
  3. c Program assumptions.
  4. d List of references.
  5. *Could not determine from available data.
  6. 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.
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Human Genomics

ISSN: 1479-7364