Ann,
    Also to your request "I'd appreciate any input about MrBayes or a similar kind of tool."

We are developing a suite of tools for phylogenetics in Galaxy. We are calling the tool suite Osiris.

We are currently adding the full tool suite to Bit Bucket:
https://bitbucket.org/repo/all?name=osiris_phylogenetics

and many tools are on the tool shed under a repository called ucsb_phylogenetics.

We are describing some of the tools here:

http://osiris-phylogenetics.blogspot.com/



We are in rather active development right now, but the RAxML tools have been used rather extensively, and allow some interactive choices (model choice, bootstrap reps, DNA v Protein, etc).  We also have a tool for BEAST (very simple, just passes the formatted xml file to run the program through Galaxy).  Another phylogenetic tree estimation tool on the tool shed (not ours) exists for GARLI.

We plan to develop a tool for MrBayes, as well, but perhaps we will not have to anymore!


Best wishes,

Todd Oakley