Nothing
## generates a pairwise sequence alignment
sim.pair.align = function(prob.matrix, init.dist, aln.len){
if (!is.matrix(prob.matrix) || (nrow(prob.matrix) != ncol(prob.matrix)))
stop("\"prob.matrix\" must be a square matrix")
if (nrow(prob.matrix) != length(init.dist))
stop("dimensions of prob matrix and init distribution do not match")
state.space = c(1:length(init.dist))
seq.table = matrix(rep(0,2*aln.len), nrow = 2, ncol = aln.len)
seq.table[1,]= sample(state.space, aln.len, replace = T, init.dist)
for (i in 1:aln.len){
seq.table[2,i] = sample(state.space, 1, replace = T, prob.matrix[seq.table[1,i],])
}
return(seq.table)
}
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