Re: [raxml] How is the outgroup assigned?

[Alexandros Stamatakis]

Dear Noe,

If --outgroup is not specified, the trees are unrooted binary trees,
what you erroneously interpret as being the root is the so-called top
level trifurcation.

See e.g. here for an explanation:
https://academic.oup.com/mbe/article/34/6/1535/3077051

Alexis


On 02.06.23 09:16, Noé Reyna wrote:
> Hello!
>
> I'm an undergrad researcher and have questions regarding the outgroup.
> While finding the bestTree and visualizing, we noticed that some of our
> samples were automatically assigned as outgroups (our Hops samples) seen
> in the attached image in lime green dots.
>
> -How does raxml-ng assign the outgroup if it's not specified via the
> --outgroup argument? I've tried looking at the github documentation and
> google and couldn't find the answer to this.
>
> -Is there a way we could run raxml-ng without an outgroup being
> specified; hence, running it using an unrooted tree? Or will we have to
> introduce an outgroup regardless in order for raxml-ng to be carried
> out? The general pipefile for this tree is: identify SNPs throughout
> samples --> use vcf2phylip to convert our multi-sample .VCF SNPs into a
> .phylip file --> input this .phy tree into raxml-ng.
>
> -I assume there's probably a way to undo the outgroup assignment w/
> other tools out there?
>
> Please let me know if there are any clarifying questions. And thanks in
> advance for the help. Much appreciated
>
> Best,
> Noe
>
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--
Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

[Noé Reyna]

Thank you for the response!!