dumb question: rapid bootstrap support value

[Luís Crespo]

Hello all,

I feel a bit embarrassed just by asking this, but I can't find a mention to this anywhere, so which is the Rapid Bootstrap support value that thresholds for a supported node in your tree? Is it the same as the Standard Bootstrap (70%)? Or higher?
I am trying to do a simple phylogenetic run using the RAxML plugin of Geneious after some years since I last run a phylogeny.

Sorry to waste your time.

Thanks in advance,

Luís

[Alexandros Stamatakis]

Dear Luis,

> I feel a bit embarrassed just by asking this, but I can't find a mention
> to this anywhere, so which is the Rapid Bootstrap support value that
> thresholds for a supported node in your tree? Is it the same as the
> Standard Bootstrap (70%)? Or higher?

That's a legitimate question:

The rapid bootstrap is intended as a fast approximation of the standard
bootstrap, so the interpretation should be the same as for the standard
bootstrap.

At https://www.biorxiv.org/content/10.1101/2024.03.04.583288v1 you can
find a recent quasi-independent (conducted in my group, but without any
biased, in favor of rapid bootstrapping, advice from my side)
re-assessment of the rapid bootstrap and other branch support methods
that might help with the interpretation.

Alexis

> I am trying to do a simple phylogenetic run using the RAxML plugin of
> Geneious after some years since I last run a phylogeny.
>
> Sorry to waste your time.
>
> Thanks in advance,
> Luís
>

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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)