Hi Chris,
I sent this message a few days ago but can't see any sign that it was
received so trying again. Apologies if anyone ends up seeing both.
To the question- in addition to the other (good) solutions given in this
thread, both HiSSE (R package) and BayesTraits (stand alone software) can
handle ASR of multi-level categorical traits.
I have used BayesTraits with option "Multi" for ASRs of traits with 3 and 4
states. Can't remember any limitations on using it for traits that take a
larger number of character states (but it was a while ago I admit).
Using HiSSE, coding your response character should be fairly
straightforward depending on the number of character states you're looking
at. If you have a trait with 4 observed states as you mention, it seems to
me that there is an implied assumption that transitions between "black" and
"white" must go through either "gray" (mixed) or "black-and-white"
(patched). In this case you can encode observed phenotypes as {00} ,{01},
{10}, {11} and disable transitions between any two states (e.g. between
{01} and {10}) based on your biological model/hypotheses.
The original HiSSE paper (Beaulieu & O'Meara 2016 Syst. Biol.) is very
clear, there is a helpful online tutorial. Nakov, Beaulieu & Alverston
(Evolution, 2019) was also useful to me.
HTH,
Roi
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