[Jalview-discuss] what does quality refer to in annotation of the alignment?

[James Procter]

Hi Deniz, sorry - I left you hanging here (I guess I was hoping someone
else might reply!).

Deniz Erturk wrote:
> Does anyone know what does "quality " exactly refer to in annotation of
> an alignment?
Its described in the online help (here:
http://www.jalview.org/help/html/calculations/quality.html) - basically
the height of the histogram at each alignment position reflects the cost
of all residue substitutions observed in the column relative to the the
sum of BLOSUM62 scores that would be obtained if the column were
completely conserved. I don't have a precise reference to hand
concerning this score, but its certainly not novel and is in essence a
local multiple sequence alignment objective function.

does that help ?
Jim