Population reconstruction from four HIV samples.

The first four columns describe the pyrosequencing data: the number of reads, the number of irredundant reads, the expected frequency (in percent) of the least frequent haplotype we can expect to cover with 99% confidence, and the number of gaps per kb in the aligned data. The next three columns describe the reconstruction algorithm: the number of non gap characters changed in error correction, the size of a minimal explaining set of haplotypes, and the diversity, measured as the expected number of amino acid differences among the estimated population. After error correction, reads were translated into amino acids. The last three columns describe the validation using (translated) clonal sequences: the number of clones sequenced, the average distance between the estimated population, and the closest Sanger haplotype, and φ1, the percentage of the estimated population that was close (up to 1 amino acid difference) to a clone.