> markov1 <- function(x,pi,P,n){
# x = vector [1 2 3 4] representing A, C, G, T, respectively
# pi = the probability distribution for X0: (1x4 row vector)
# P = transition matrix (4x4)
# n = length of simulated sequence
# Initialize vector to contain simulated sequence
mg <- rep(0,n)
# Produce initial element
mg[1] <- sample(x,1,replace=TRUE,pi)
for(k in 1:(n-1)){
mg[k+1]<-sample(x,1,replace=T,P[mg[k],])
}
return(mg)
}