The use of np.int8 in the matrices.py script limits the maximum sequence length that can be processed to 127, which restricts distance calculations for longer sequences. I am noting this for users who handle longer sequences and may not notice that the calculated distances are wrong, since the code does not throw a warning or an error, but calculates the metric wrongly. The int type should be altered (either manually or dynamically by code) when sequences longer than 127 are used.
Thank you for this helpful package, Andrew!