Open jbarnoud opened 9 years ago
I think we can use the "gapopen" value used for structural alignement if a real PB is in front of Z, while it is zero if Z in front of Z. cc @pierrepo @jbarnoud
OK. How much is a gapopen value ?
-600 !!! Ok, it is x 100 ...
As noted in a comment to #56, the substitution score from and to the Z dummy block is always 0. This is used in
PBclust
to build the distance matrix, and to compare sequences with the--compare
option.To this, @pierrepo commented:
How to we want to handle substitution from and to the Z dummy block ? The obvious way, as suggested by @pierrepo is to raise an exception. Yet, this means that we cannot do a clustering when some information is missing, or that we need to find tricks.
Bare in mind that this will affect how we calculate distance matrices. See #62 for more about distance matrix calculations.
cc @pierrepo @alexdb27