Skip to main content

Table 1 Haplotype reconstruction performance on simulated datasets

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

Dataset

Nucleotide

No. of haplotypes

Mean Hamming

MHD of top 4

Range Hamming

 

diversity

reconstructed

distance (MHD)

haplotypes

distance

U1

1

9

6

6

(6-6)

U2

2

9

4.33

2.25

(1-9)

U4

4

9

4.33

2

(2-9)

U10

10

9

4.66

2.25

(1-9)

L1

1

6

49.5

28.25

(11-93)

L2

2

5

46.2

23

(7-139)

L4

4

9

158.44

11

(1-427)

L10

10

7

283.85

65.25

(46-706)

LHV

1+

9

20.66

13.5

(13-37)

  1. Simulated datasets were named according to the frequency distribution of their population and their nucleotide diversity. Populations with uniform and log-normal frequency distributions are labeled as U and L, respectively, followed by a number denoting the percentage nucleotide diversity between genomes. In all cases there were 9 “true” genomes.
Back to article page

Retrovirology

ISSN: 1742-4690

Contact us