Benneth has tested ScafosPy and found the "Longest sequence" and "Ambiguity" modes to work well. However, he could not get the "Lowest Divergence" mode to work well. This is a quite important mode, so it is important to have it function well. Apparently, in a protein sequence like this:
EYQRSG
EAQSSG
EAQRSQ
the program would only keep the amino acid positions 1, 3 and 5 (with identical positions in all sequences: EQS) but would completely remove (from the output sequence) the positions 2, 4 and 6 (where it should select based on a "majority rule, i.e., ARG).
Not sure where the problem is, and I am not sure if Benneth tested it for nucleotide sequences as well, but this is a rather serious bug that should be removed with priority.
Benneth has tested ScafosPy and found the "Longest sequence" and "Ambiguity" modes to work well. However, he could not get the "Lowest Divergence" mode to work well. This is a quite important mode, so it is important to have it function well. Apparently, in a protein sequence like this:
EYQRSG EAQSSG EAQRSQ
the program would only keep the amino acid positions 1, 3 and 5 (with identical positions in all sequences: EQS) but would completely remove (from the output sequence) the positions 2, 4 and 6 (where it should select based on a "majority rule, i.e., ARG).
Not sure where the problem is, and I am not sure if Benneth tested it for nucleotide sequences as well, but this is a rather serious bug that should be removed with priority.