Correlation between multistate characters


#1

Are there phylogenetic comparative methods/software for testing correlation between characters that have multiple states. BayesTraits only deal with binary characters.


#2

You can create arbitrary numbers of states in BEAST. The trick is to follow the discrete trait examples. Load up traits called AA, AB, AC, BA … etc. You can parameterize the rate matrix as you like too (i.e., just concerted changes or independent changes as 2 parameters or something more complex).


#3

A general framework in BEAST to assess correlations between multiple types of data (including multistate data) is described here: http://arxiv.org/abs/1406.3863