Reorders the rows and columns of matrices to agree with the order used in cold.
usage:
reordermatrix codonfile inputfile outputfile
codonfile (see codonlistexample.txt for an example) lists the codons in the the order of the rows and columns of the matrices in inputfile, which consists of just a list of matrices. reorderMatrix then reorders the rows and columns to the order used by cold (see coldcodonorder.txt), in the file called outputfile.