This website has a VERY comprehensive list of phylogeny programs, and allows you to filter by method (for example Bayesian). I'm sure at least one of these programs will be able to do what you want

http://evolution.genetics.washington.edu/phylip/software.html

BayesTraits can utilize either discrete or continuous data

http://www.evolution.rdg.ac.uk/BayesTraits.html

Thanks Robert and Kevin. I will look more into it. Im just afraid that this programs are mostly used to do ancestral character reconstruction over a phylogeny rather than reconstruct a topology with them. 

Melissa, it seems that MrBayes can do what you ask. I have never tried that, but at least there is an option for specifying continuous characters in the input nexus file ("Datatype = Continuous"):

http://mrbayes.sourceforge.net/Help/format.html