Outgroups

[bko...@uni-potsdam.de]

Hi,

is there a opportunity to define one species as an outgroup by using RAxML as Tree Estimator?

Thanks for the help
Ben

[Mark Holder]

Hi,

I don't think that there is a way to do that right now. 

I may be incorrect on that because I do recall that there is some syntax for passing in arguments to RAxML in a "raw" form. Those options are not well documented, and are a bit prickly to use.

However if you are using a time-reversible tree inference in RAxML (as SATe's use RAxML does), then the rooting position can be applied to the tree after it is inferred. Under time-reversible inference, the rooting position does not alter the score of the tree. So in these contexts, the outgroup setting is essentially a convenience to let the tree be displayed in the correct rooting. Tools like FigTree will let you correct the rooting after the analysis. So that is a workaround for SATe not passing along an outgroup option to RAxML, but to correct the rooting after the analysis is done.

all the best,

Mark

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