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_116
Snippet: We compare the topology of dendrograms obtained from HLA selection profiles to dendrograms obtained from human HLA protein sequence information from the IMGT database [33] . To obtain a dendrogram based on host HLA sequence information for comparison, we first remove identical HLA protein sequences in the available sequenced region and restrict analysis to the first four members of each 2-digit HLA type for which we have estimated an HLA selectio.....
Document: We compare the topology of dendrograms obtained from HLA selection profiles to dendrograms obtained from human HLA protein sequence information from the IMGT database [33] . To obtain a dendrogram based on host HLA sequence information for comparison, we first remove identical HLA protein sequences in the available sequenced region and restrict analysis to the first four members of each 2-digit HLA type for which we have estimated an HLA selection profile for HIV-1. We use RaxML [11] to obtain maximum likelihood trees for each of the three class I molecules. As we expect, members of the same 2-digit HLA type cluster together.
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