As parameter cost increase results diverge increasingly
from those under different costs (Table 2). However,
this trend is neither proportional nor monotonic.
For a constant gap cost, both RLI and percent shared
clades suggest that doubling the transition/transversion
ratio (ts/tv) from 1 to 2 has more effect than from 2 to 4
(where similarity to the reference analysis actually improved
under gap cost 1). For constant ts/tv ratio,
trends vary: at ts/tvผ1, doubling gap costs loses about a
third of shared clades each time, but at 2 and 4 doubling
gap cost increases both measures but quadrupling it
decreases both. In any case, results are quite sensitive to
parameter choice: roughly 50% of the reference clades
are lost if any value is changed.