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_33
Snippet: Within the MCMC, we have three main classes of move. Moves to alter a parameter at a single site or window of sites, moves to merge or split windows, and moves to expand and contract selection windows to push them around the genome. When adding HLA-associated selection to our codon model of substitution, we considered separate parameters to scale selection away from consensus in the presence of each host HLA type at each site (γ h,i ), and param.....
Document: Within the MCMC, we have three main classes of move. Moves to alter a parameter at a single site or window of sites, moves to merge or split windows, and moves to expand and contract selection windows to push them around the genome. When adding HLA-associated selection to our codon model of substitution, we considered separate parameters to scale selection away from consensus in the presence of each host HLA type at each site (γ h,i ), and parameters to model reversion towards consensus at each site (ζ i ). In order to increase speed we alter these parameters within selection windows in our MCMC scheme. The selection windows that we discuss are analogous to the selection windows and recombination windows described in [4] . We now introduce some notation:
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