Hi Jim, Peter, et.al. Not exactly sure which list is most appropriate for this, so I'll start with both.
Now that I've gotten past the hurtle of getting jabaws installed locally (and we're moving forward with our DAS server to pass gene family data to Jalview), I wanted to resume discussions we first had back in 2011 regarding adding phylogenetic services to Jalview. At that time, Jabaws was in mid-transition from 1.x to 2.0, so I wanted to make sure my group re-engages on this a good picture of where things stand. -silly question, but I wanted to verify that there hasn't yet been a complete or partial integration of GBlocks, or any ML phylogenetic package (e.g, RAxML) into jabaws and jalview? -is the thinking still that GBlocks should be a web service implementing the SequenceAnnotation interface? -and the recommended way of adding a phylogenetic component is as a web service? Rather than being directly incorporated in the "Calculate Tree" set of NJ and Avg.Dist. tree builders in the Alignment Frame top menu? I imagine the answer is yes, if only to be able to execute cpu intensive phylo algorithms on bigger server-side hw, but I still wanted to check. -is there additional documentation, besides the old threads with Joni in my group, for adding services to jabaws? -you already have clients for tree rendering, with the ability to display bootstraps. I assume that would be client invoked to display results from a "tree build as web service" run? Or is there anything special about clients that handle web service output vs. others? Also, just curious if there is someone currently on the Jalview project with exclusive or majority focus on Jabaws, now that Peter has moved on? best, -David -- David M. Goodstein, Ph.D. Phytozome Group Lead Plant and Computational Genomics Group Joint Genome Institute - U.S. Dept. of Energy Center for Integrative Genomics - UC Berkeley
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