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_60
Snippet: In each case, we assume that the consensus 'wild type' strain is correctly defined and set any nonsynonymous difference from consensus as escape. For methods 2, 4 and 5, we determine a maximum likelihood estimate of the underlying genealogy using RAxML version 8.2.11 [11] . Methods 1, 3 and 6 do not require an estimate of the genealogy. We now briefly summarise each of the compared methods......
Document: In each case, we assume that the consensus 'wild type' strain is correctly defined and set any nonsynonymous difference from consensus as escape. For methods 2, 4 and 5, we determine a maximum likelihood estimate of the underlying genealogy using RAxML version 8.2.11 [11] . Methods 1, 3 and 6 do not require an estimate of the genealogy. We now briefly summarise each of the compared methods.
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