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 [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/