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_63
Snippet: PhyloD We implement the methods of Carlson et al. as described in [9] . As described above, we determine an estimate of the maximum likelihood tree, G max using RAxML [11] before using likelihood ratio tests to compare models conditional on the maximum likelihood tree. The initial null model at each site is a simple two state model described by two parameters -the mutation rate; λ, and the stationary probability of observing the wild-type amino .....
Document: PhyloD We implement the methods of Carlson et al. as described in [9] . As described above, we determine an estimate of the maximum likelihood tree, G max using RAxML [11] before using likelihood ratio tests to compare models conditional on the maximum likelihood tree. The initial null model at each site is a simple two state model described by two parameters -the mutation rate; λ, and the stationary probability of observing the wild-type amino acid; π. The associated instantaneous rate matrix is
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