Performance of local haplotype reconstruction.

For all four experiments, we report the total number of predicted haplotypes (column Reconstructed), the number of correct haplotypes (true positives, TP), the number of reconstructed haplotypes that do not match any of the original clones (false positives, FP), and the number of missed haplotypes (false negatives, FN). This number is equal to 10 – TP, because ten is the total number of haplotypes present in the sample. Sensitivity is defined as TP/(TP+FN) and specificity as TP/(TP+FP). Local haplotype reconstruction was performed on the 252 bp region of the HIV pol gene coding for protease amino acids 10 to 93 for the 454/Roche data, and on the 35 bp subregion of highest entropy for the Illumina reads.