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Table 4 Precision of haplotype reconstruction algorithms

From: Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants

Algorithm

U2

U4

U10

L2

L4

L10

LQ4_1

PredictHaplo [53]

1

1

1

0.60

0.44

0

0.57

ShoRAH [38]

0.10

0.18

0.39

0

0

0

0

QuRe [37]

0

0

0.01

0

0

NA

0

  1. We calculated the precision by taking the ratio between the number of accurately reconstructed haplotypes over the total number of reconstructed haplotypes. An haplotype was considered to be accurately reconstructed if the Hamming distance to the “true” genome was ≤25. Recall values are not listed as most of them are 0 for ShoRAH and QuRe.