Phylogenetic data

[embaldridge]

Dendropy seems to be really slow when working with the supertrees, if it is even working at all. I need to find a faster way to work with the supertrees that will let me check the list of taxa against the other data that I have, and eventually get a list of distances to use as a variable in my analyses.

[embaldridge]

Asked Ben, got a recommendation for the following tools:
BioPython
PhyloCommons (http://www.phylocommons.org)

[embaldridge]

BioPython seems to be working, need to write script that pulls out the taxon names.

[embaldridge]

Okay, so the full trees seem to be running really slowly, and I don't need the full trees anyway, maybe I should consider pruning the trees with the PhyloCommons tool first and then doing stuff to them.

[embaldridge]

Proposed flow: Get list of species names from query outputs. Query PhyloCommons with list, after getting list of names into the right format for the URL, which is going to be ridiculously long. Get results back from PhyloCommons. Stuff distances with names into table. and save output. Associate species names with phylogenetic distances in original query. Save modified file. I think after this point, I will be able to start calculating occupancies for species and things like that.