One thing that bothers me about decay indices is what to make of a particular
value for a clade. Say that a particular clade will "decay" at three steps.
Is that a large number or a small number? In other words, should I put a lot
of confidence in clades that decay at three, four, five, ... steps?
Faith has proposed randomization of the original matrices to determine
the null distribution of the decay indices (his T-PTP tests; we need to talk
to him about acronyms...). However, passing the "is it random" test seems
like a pretty easy test for most data sets to pass.
John
