log-odds on a drift model: what one substitution costs

log-odds on a drift model: what one substitution costs

The rule is the log-odds of one step of a random walk that stays put with probability 0.6 and otherwise moves, eight times more readily within a purine or pyrimidine pair than between them; a gap character costs 2. Read a row as the symbol expected and a column as the symbol seen; the entry is what the table charges for that pair, in bits. The diagonal is zero by construction so that a minimising fill can be used unchanged. Nothing here is copied from a published table: every entry is computed from the rule beside it, which is the difference between a matrix that can be checked and one that can only be quoted.

Drawn at 700 × 326, wide on the page. Everything above is what cost-model returns with no arguments; the caption is the generator's own, computed from the numbers in the drawing rather than written beside it.

10 essays call cost-model. The drawing above is what it returns with no arguments at all; every call below passes it something, because a placement that passes nothing draws whichever member of the family the generator happens to default to rather than the one its essay argues about — which is what optcheck and figfill exist to catch.