This directory contains helpful Octave (Matlab clone) code.

File and contents:
paml2fastprot

	One function for converting a PAML matrix to "classic"
	Markov-chain transition matrix format ("a Q matrix"). We would
	probably be better off being able to read a PAML matrix
	natively, but for simplicitly we are using this
	workaround. The second function in this code outputs the Q
	matrix in a format suitable for direct inclusion in the
	code. Look at the FastProt class ModelMatrix for examples of
	how to add a matrix, it is quite self-explanatory.

