DUMMY and DUMMY2 models

[Rob Lanfear]

Hi All,

Can anyone throw any light on the origin of the DUMMY and DUMMY2 amino acid replacement matrices in RAxML?

They seem to be defined just like all the other models (https://github.com/stamatak/standard-RAxML/search?utf8=%E2%9C%93&q=DUMMY2&type=Code), but when I search online I can't find anything about them. 

The real question is: should they be included in standard model selection software like PartitionFinder, or are they placeholders that should be ignored?

May thanks,

Rob

[Alexandros Stamatakis]

Dear Rob,

If I remember correctly these models represented some improvement of I
think the MTMAM model (not sure though) that some Japanese colleagues
asked me to add to RAxML for some sort of paper.

They howeber never got back to me about this again.

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

[Rob Lanfear]

Thanks Alexis. I think I'll take them out of PartitionFinder, since there doesn't seem to be any published reference to them.

Cheers,

Rob

[Alexandros Stamatakis]

yes, take them out,

alexis

On 04.12.2016 00:10, Rob Lanfear wrote:
> Thanks Alexis. I think I'll take them out of PartitionFinder, since
> there doesn't seem to be any published reference to them.
>
> Cheers,
>
> Rob
>
> On Saturday, 3 December 2016 21:55:00 UTC+11, Alexis wrote:
>
> Dear Rob,
>
> If I remember correctly these models represented some improvement of I
> think the MTMAM model (not sure though) that some Japanese colleagues
> asked me to add to RAxML for some sort of paper.
>
> They howeber never got back to me about this again.
>
> Alexis
>
> On 02.12.2016 10:15, Rob Lanfear wrote:
> > Hi All,
> >
> > Can anyone throw any light on the origin of the DUMMY and DUMMY2
> amino
> > acid replacement matrices in RAxML?
> >
> > They seem to be defined just like all the other models
> >
> (https://github.com/stamatak/standard-RAxML/search?utf8=%E2%9C%93&q=DUMMY2&type=Code

> <https://github.com/stamatak/standard-RAxML/search?utf8=%E2%9C%93&q=DUMMY2&type=Code>),

>
> > but when I search online I can't find anything about them.
> >
> > The real question is: should they be included in standard model
> > selection software like PartitionFinder, or are they placeholders
> that
> > should be ignored?
> >
> > May thanks,
> >
> > Rob
> >
> > --
> > 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>