Levitsky consensus algorithm problems

Problem 1 (no scenario):

Levitsky consensus algorithm takes in account all alignment bases (not only in one colum), but these values are not being updated when alignment is being edited (in any way).

Problem 2:

1. Open bug.aln (see attachments)
2. Set Levitsky consensus algorithm
3. Set threshold to 75
   Expected: Second column has Y
   Current: Second column has B (C + G + T)

This problem happens because algorithm considers symbols on DNA extended in alphabetical order, but it should be in order of coding symbol numbers:

1. A, C, G and T - separate nucleotides
2. R, Y, S, W, K and M - code 2 nucleotides
3. B, D, H anv V - code 3 symbols
4. N - codes 4 symbols