On Oct 29, 2012, at 3:20 PM, Todd Oakley <todd.oak...@lifesci.ucsb.edu> wrote:

> 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

This is an interesting project. I'm glad to see more people working on 
phylogenetics related wrappers and workflows. I wonder if we could get a 
"Phylogenetics" category added to the main Galaxy Toolshed, so we could put all 
the relevant wrappers in there to make them easier to find considering the 
apparent duplication of efforts.


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