Author: Palmer, Duncan S.; Turner, Isaac; Fidler, Sarah; Frater, John; Goedhals, Dominique; Goulder, Philip; Huang, Kuan-Hsiang Gary; Oxenius, Annette; Phillips, Rodney; Shapiro, Roger; Vuuren, Cloete van; McLean, Angela R.; McVean, Gil
Title: Mapping the drivers of within-host pathogen evolution using massive data sets Document date: 2019_7_9
ID: 100r7w2n_71
Snippet: All sequences and their associated host drug regime data were downloaded from the Stanford drug resistance database [22] . We used the alignments provided, though sites at which there was ≥5% ambiguity were removed, followed by sequences for which there was ≥5% nucleotide ambiguity across the region of interest. In reverse transcriptase a ∼550 nucleotide region is sequenced much more frequently than the remainder of the gene and we wish to .....
Document: All sequences and their associated host drug regime data were downloaded from the Stanford drug resistance database [22] . We used the alignments provided, though sites at which there was ≥5% ambiguity were removed, followed by sequences for which there was ≥5% nucleotide ambiguity across the region of interest. In reverse transcriptase a ∼550 nucleotide region is sequenced much more frequently than the remainder of the gene and we wish to retain power to estimate parameters. One sequence per patient was included in the combined alignment of reference and query data sets by removing repeat entries of any given patient identifier uniformly at random (assuming unique patient identifiers ⇒ unique patients).
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