Site-specific frequency models: IQtree vs RAxML

[Christian Rinke]

Hi,

We were using IQtree with the new posterior mean site frequency (PMSF)

model – it’s a fast approximation to the computational demanding

profile mixture models C10 to C60 (see here: http://www.iqtree.org/doc/Complex-Models )

I was wondering is there a similar model in RAxML/ExaML?

Best,

Chris

[Alexey Kozlov]

Hi Chris,

not at the moment, but it's on our TODO list...

Best,
Alexey

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[Christian Rinke]

Thanks Alexis,

Is there an overview of all the protein models available in RAxML/ExaML.

I was wondering if there is anything like the the IQ tree C10 -C60 models?

Best,

Chris

On Monday, 25 March 2019 09:09:29 UTC+10, Alexey Kozlov wrote:

Hi Chris,

not at the moment, but it's on our TODO list...

Best,
Alexey

On 24.03.19 23:22, Christian Rinke wrote:
> Hi,
>
> We were using IQtree with the new posterior mean site frequency (PMSF)
>
> model – it’s a fast approximation to the computational demanding
>
> profile mixture models C10 to C60 (see here:
> http://www.iqtree.org/doc/Complex-Models )
>
>
> I was wondering is there a similar model in RAxML/ExaML?
>
>
> Best,
>
> Chris
>
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> You received this message because you are subscribed to the Google
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> <mailto:ra...@googlegroups.com>.

[Alexandros Stamatakis]

It's specified in the manual but you will also get a listing if you use
the terminal help command -h

The C10 - C60 models are not available in ExaML/RAxML either, as Alexey
said it's on our TODO list for RAxML-NG,

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

www.exelixis-lab.org