asc-corr=stamatakis

[Hollie Hatherell]

Hi,

I'm trying to run raxml with --asc-corr=stamatakis and I'm unsure of what the specification of p4=1-1000 represents in the example in the manual, and what I should put here if I just want one partition.

Thanks,
Hollie

[Alexandros Stamatakis]

p4=1-1000 represents the start and end site of a partition, if you just
have one single partition anyway, starting at position 1 (evidently) and
ending at position 278, you just specify one line in the partition file,
e.g.,

myOneAndOnlyPartition=1-278

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

[Hollie Hatherell]

Thanks for you reply. Just one more question: what defines the end position of the partition? I'm running this with the variable sites from my DNA data - so would the end be the number of variable sites I have?

Thanks,
Hollie

[Alexandros Stamatakis]

> Thanks for you reply. Just one more question: what defines the end >
position of the partition? I'm running this with the variable sites from
> my DNA data - so would the end be the number of variable sites I have?

yes,

alexis

>
> Thanks,
> Hollie
>
> On Friday, 5 February 2016 14:31:05 UTC, Alexis wrote:
>
> p4=1-1000 represents the start and end site of a partition, if you just
> have one single partition anyway, starting at position 1 (evidently)
> and
> ending at position 278, you just specify one line in the partition
> file,
> e.g.,
>
> myOneAndOnlyPartition=1-278
>
> alexis
>
> On 05.02.2016 15:26, Hollie Hatherell wrote:
> > Hi,
> >
> > I'm trying to run raxml with --asc-corr=stamatakis and I'm unsure of
> > what the specification of p4=1-1000 represents in the example in the
> > manual, and what I should put here if I just want one partition.
> >
> > Thanks,
> > Hollie
> >
> > --
> > You received this message because you are subscribed to the Google
> > Groups "raxml" group.
> > To unsubscribe from this group and stop receiving emails from it,
> send

> > an email to raxml+un...@googlegroups.com <javascript:>
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.

> > For more options, visit https://groups.google.com/d/optout

> <https://groups.google.com/d/optout>.

>
> --
> 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>

[Hollie Hatherell]

Many thanks,

Hollie