To run the code, please download all the files in a directory.
Then run:
[alignment vpath] = viterbiPathPair(fileName1, fileName2);
in Matlab where fileName1 is the name of the file containing input 1 and fileName2 contains input 2.
'alignment' now contains the alignment of the two sequences in reverse order. A '1' refers to 'A', '2' to 'C', '3' to 'G' and a '4' to a 'T' and a '-1' refers to a deletion at that position.
'vpath' contains the viterbi path (i.e. the sequence of states) of the alignment in reverse order (from back to front).