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_18
Snippet: . Let the probability of copying the codon at position j from sequence i be denoted ε i,j . This is the probability of an observed state given a hidden state, and is known as an emission probability in the language of HMMs. Then f i,1 is just an emission probability and easily computed if we have a uniform prior on the SCF at the first position. We then calculate f i,j for j ≥ 2 recursively as follows:.....
Document: . Let the probability of copying the codon at position j from sequence i be denoted ε i,j . This is the probability of an observed state given a hidden state, and is known as an emission probability in the language of HMMs. Then f i,1 is just an emission probability and easily computed if we have a uniform prior on the SCF at the first position. We then calculate f i,j for j ≥ 2 recursively as follows:
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