fephyfofum/gophy

gophy's Issues

Can't run the bp

Hello,
I would like to run bp but getting following error. Any idea how to fix it? Thanks

➜  ~ go get github.com/FePhyFoFum/gophy
# github.com/FePhyFoFum/gophy
go/src/github.com/FePhyFoFum/gophy/nuclikeoptimize.go:49:10: settings.FunctionThreshold undefined (type optimize.Settings has no field or method FunctionThreshold)
go/src/github.com/FePhyFoFum/gophy/nuclikeoptimize.go:56:10: settings.FunctionConverge undefined (type optimize.Settings has no field or method FunctionConverge)
go/src/github.com/FePhyFoFum/gophy/nuclikeoptimize.go:107:10: settings.FunctionThreshold undefined (type optimize.Settings has no field or method FunctionThreshold)

comments in node.go

need to add comments for the additional node.go properties that are not clear (LAD,FAD, etc.)

-tv option in bp

Hello,
In the https://fephyfofum.github.io/gophy/ you mentioned to use -tv option, but when I add it, bp gives not defined error. flag provided but not defined: -tv

Would you please fix it, or other workaround to get list of trees with the conflict, concordance, and uninformative?

I should mention that the option works on mac, but not in the linux cluster. I am not sure why? I have 2 cores in macbook, so prefer to run on cluster.

Thanks
Mohammad