JAL-2397: Correct PCA (Jalview/SeqSpace) and substitution matrix based tree...
|Participant||Role||Time Spent||Comments||Latest Comment|
|Reviewer - Complete||21m||3||I've outlined how this could be done in CR-JAL-33.|
Tree distances calculation uses column 23 of the Blosum62 matrix to score char-gap (as -4) or gap-gap (as +1).
PCA calculation uses column 22 (residue 'X') which scores 0 for A/S/T and -1 or -2 for other residues (-1 for X-X).
a) should these be consistent?
b) should they both use zero for gap scores?
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