Nothing
cai <- function(seq, w, numcode = 1, zero.threshold = 0.0001, zero.to = 0.01){
stops <- which("Stp" == aaa(translate(s2c(c2s(words())), numcode = numcode)))
singulets <- which(sapply(syncodons(words(), numcode = numcode), length) == 1)
exclude <- c(stops, singulets)
w <- w[-exclude]
w[w < zero.threshold] <- zero.to # if value is effectively zero make it 0.01
nncod <- uco(seq)
nncod <- nncod[-exclude]
sigma <- nncod %*% log(w)
exp(sigma/sum(nncod))
}
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