A square matrix object of dimension n x n where n is the
number of states, and element [i,j] is the rate of
transition from state i to state j
eq.freq
A vector of length n giving the equilibrium
frequencies of each state. If NULL, calculate equilibrium frequencies
that will make a reversible markov chain.
begin.freq
A vector of length n giving the initial state
frequencies. If NULL, use equilibrium frequencies.
end.freq
A vector of length n giving the final state frequencies.
If NULL, do not condition on end frequencies.