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