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naturalis / supersmart

Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa
MIT License
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Constraint trees in bbinfer #104

Closed hettling closed 7 years ago

hettling commented 7 years ago

It would be good if monophyly could be constrained in bbinfer for Raxml (and Examl) if possible using constraint trees.

rvosa commented 7 years ago

This can apparently be done in raxml (not the light version), see here: http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html

hettling commented 7 years ago

Constraining genera for Raxml backbone inference is now possible with option -c or --constrain_genera (--cheat), committed to the devel branch.

Unfortunately, Examl and Exabayes do not offer this option. For Bayesian inference, this could be done in MrBayes but there is so far no wrapper (but we can export MrBayes style supermatrices with smrt bbmerge).

rvosa commented 7 years ago

Also see #82

hettling commented 7 years ago

RaXML constraint trees are implemented, and we still have #82 for constraints in future ExaBayes versions, therefore closing this.