For the purpose of screening indices (no matter the biological relevance on alignments at this point), we could compute the AC (amino/keto) , AG (purine/pyrimidine) and AT (weak/strong) skews (x-y)/(x+y) from the substitution matrix…
Given that we have no control on the orientation of the aligned scaffolds, it may be needed to average the absolute values for each pair of target and query scaffolds, perhaps normalising by alignment length…
Alternatively or in parallel, one could extend it to a more pairwise view, computing AC* and AG* just like GC* equilibrium (f56c4d8).
For the purpose of screening indices (no matter the biological relevance on alignments at this point), we could compute the AC (amino/keto) , AG (purine/pyrimidine) and AT (weak/strong) skews
(x-y)/(x+y)from the substitution matrix…Given that we have no control on the orientation of the aligned scaffolds, it may be needed to average the absolute values for each pair of target and query scaffolds, perhaps normalising by alignment length…
Alternatively or in parallel, one could extend it to a more pairwise view, computing AC* and AG* just like GC* equilibrium (f56c4d8).