Define multiple outgroups that are monophyletic

[Kelsey Pugh]

Hi again,

I am trying to define multiple taxa as a monophyletic outgroup. I usually use the FORCE+ command to define multiple outgroups in TNT, but this makes them sequential and not monophyletic. I think that this might be possible by defining taxonomy (i.e. the 2 outgroups will  be labeled as NWM), but I have never used the TAXONOMY command and can't find an example online. Does anyone have any experience doing this/ know another way to constrain a monophyletic outgroup?

Thanks in advance for any advice,
Kelsey

[Martin Smith]

As far as I know TNT always roots the tree on a single taxon: there's no way to force a multi-taxon outgroup.

Of course, it is easy to change the position of the root in other tree visualisation software, and the position of the root is irrelevant to analysis. 

My solution therefore would be to force the INGROUP to be monophyletic, which is equivalent to forcing the outgroup to be monophyletic if you root the tree on the node between the ingroup and outgroup.

[Kelsey Pugh]

Hi Martin,

Thanks for your reply. I was under the impression that order of the outgroups would result in topological differences in the ingroup, but thanks for correcting me. I will run with the ingroup monophyltic and re-root.

Kelsey

[Miguel Moreno-Azanza]

If you enable taxonomy, You can root your trees using a taxonomy outgroup (just for the visualization, not for the search, which will always consider a single outgroup). This will do the trick most of the times

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[Steven Vidovic]

You could try running the outgroup on its own, calculate the ancestral states and then code a taxon called ROOT with those states.

On Wednesday, 26 August 2015 18:03:58 UTC+1, Kelsey Pugh wrote: