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
Search related documents:
Co phrase search for related documents- amino acid and likelihood tree: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
- amino acid and maximum likelihood tree: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
- amino acid and mutation rate: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
- amino acid and null model: 1, 2, 3, 4
- amino acid and ratio test: 1, 2, 3, 4, 5, 6
- amino acid and state model: 1, 2, 3
- likelihood ratio test and mutation rate: 1
- likelihood ratio test and null model: 1, 2, 3, 4, 5
- likelihood ratio test and ratio test: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
- likelihood ratio test and site null model: 1
- likelihood ratio test and state model: 1
- likelihood tree and maximum likelihood tree: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
- likelihood tree and maximum likelihood tree estimate: 1
- likelihood tree and mutation rate: 1
- likelihood tree and ratio test: 1
- maximum likelihood tree and mutation rate: 1
- mutation rate and null model: 1
- mutation rate and parameter mutation rate: 1, 2, 3
- mutation rate and ratio test: 1, 2
Co phrase search for related documents, hyperlinks ordered by date