The code is included in the seq.alg module and it is documented (with an
example) in seqalg.rst. The main new functions are:
- clip_start = seq.alg.ClipAlignment(aln)
- d_map = seq.alg.CreateDistanceMap(aln)
- var_map = seq.alg.CreateVarianceMap(d_map)
- dist_to_mean = seq.alg.CreateDist2Mean(d_map)