rapid bootstraps

[chris blair]

Hi everyone, 

I am running a combined rapid bootstrap + ML analysis on a large partitioned alignment using the hybrid MPI/Pthreads version of RAxML. In my script I instructed RAxML to run 100 rapid bootstraps, but for some reason it ran 128. Any idea why? Does this have something to do with the MPI parallelization?

Chris

[Alexandros Stamatakis]

yes it's associated with MPI, depending on how many nodes and how many
replicates you specify it might compute some more reps than actually
requested ... there should also be some older posts about this behaviour
on the group ...

alexis

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[chris blair]

Thanks. Did anyone send an alignment your way yet? I may have something that you can use.

Chris

[Alexandros Stamatakis]

no, not yet, I'd be really grateful for such an alignment :-)

alexis

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>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> University
> of Arizona at Tucson
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>