Prepare example case - Githubissues

rvosa commented 10 years ago

make a documented step-by-step tutorial
run all intermediate steps

rvosa commented 10 years ago

So far, have created examples/gentianales directory with name list and calibration table.

rvosa commented 10 years ago

Have added a name list: examples/gentianales/gentianales.txt and two (questionable) fossil tables. Maybe @alexantonelli and Ruud can sort out which to use (this also ties in with issue #7).

rvosa commented 10 years ago

For the primates we have now gone through the following steps:

perform TNRS on the input names (taxosaurus)
align all relevant phylota clusters (mafft)
merge the clusters into superclusters using reciprocal BLASTing (blast/muscle)
construct supermatrix for exemplar set of taxa
infer backbone tree on supermatrix (exaML)
calibrate backbone tree (treePL)
construct genus-level, multi-species, multi-locus coalescent trees (*BEAST)

Still to do: graft genus-level trees onto backbone. We basically almost have all the steps, but they need to be tested more, cleaned up, etc.

rvosa commented 10 years ago

I think this is a redundant issue, we have decent example cases. I am closing this.

naturalis / supersmart

Prepare example case #2