use common _runner method to run phyml.  add run()
use common _runner method to run phyml.  add run()

ngcrawford/CloudForest,jonchang/CloudForest,ngcrawford/CloudForest,jonchang/CloudForest,ngcrawford/CloudForest,jonchang/CloudForest,jonchang/CloudForest,ngcrawford/CloudForest,ngcrawford/CloudForest