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Table 1 Correlation between the true haplotype frequencies and those estimated by five programs

From: Haplotypic structure of the X chromosome in the COGA population sample and the quality of its reconstruction by extant software packages

  Series Locationa Lengthb #Hapc D* Arlequin (EM)d Phase (CP)e Snp Hap (EM) Haplo Block (BN)f Haplo typer (D)g
5-marker haplotypes 1 55,992,117 0.14 3 1 1 1 1 1 1
  2 10,464,050 0.14 10 0.6 1 1 1 1 1
  3 54,499,735 1.42 5 0.59 1 1 1 1 1
  4 71,732,319 2.62 8 0.46 1 1 1 1 1
  5 36,765,524 0.13 11 0.36 1 1 1 1 1
  6 84,938,832 1.46 9 0.28 0.97 0.99 0.97 0.98 0.89
  7 42,260,770 4.25 20 0.19 0.95 0.99 0.96 0.95 0.92
  8 90,806,576 2.23 16 0.18 0.94 0.96 0.94 0.83 0.92
  9 63,668,482 3.84 30 0.05 0.84 0.95 0.82 0.75 0.77
  10 3,562,850 3.86 31 0.02 0.75 0.91 0.75 0.67 0.65
10-marker haplotypes 11 54,499,735 1.63 6 0.74 1 1 1 1 1
  12 55,920,880 10.51 15 0.44 0.99 1 0.98 0.93 0.97
  13 74,309,896 10.79 130 0.02 0.51 0.78 0.50 0.07 0.50
  14 14,437,620 13.36 165 0.02 0.14 0.35 0.19 0.25 0.17
  1. anucleotide position of the first marker of the haplotype
  2. blength of the haplotype (Mb)
  3. cnumber of different haplotypes in the sample
  4. dEM: expectation-maximization algorithm
  5. eCP: coalescent prior
  6. fBN: Bayesian networks
  7. gD: Dirichlet prior