[Biopython-dev] Biopython tutorial: Substitution Matrices

[Hui Ting Grace Yeo]

Hey everyone,

I'm working on this bug here https://redmine.open-bio.org/issues/3340 and I've updated the example in the tutorial (on substitution matrices, 17.4.2) using Bio.AlignIO on github here https://github.com/yhtgrace/biopython/tree/clustalw-alignIO-replace. I'm able to reproduce the dictionary replace_info, but when I go on to finish the example, I get the following log odds matrix:

D   2
E  -1   1
H  -5  -4   3
K -10  -5  -4   1
R  -4  -8  -4  -2   2
   D   E   H   K   R

which is different from the one given in the tutorial. I'm wondering if I've missed something. 

Thanks!
Grace Yeo