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

Table 3 Comparison of haplotype reconstruction algorithms

Simulated viral populations given in Tables 1 and 2 were also analyzed by two alternative haplotype reconstruction algorithms, i.e., ShoRAH and QuRe [33, 37, 38]. All datasets contained 9 “true” genomes. NA indicates that QuRe was terminated after two weeks of CPU run time (3.1 GHz 16 core Intel Xeon processor, 128GB RAM).

ISSN: 1742-4690