AUTO protein model for normal RAxML

[siavash mirarab]

RAxML light has an option that enables automatic selection of the protein model. I am just wondering if this feature is available in the normal RAxML as well? If not, is there a plan to add it to the normal RAxML?

[Alexis]

This option is currently not available in standard RAxML and it is not
on my priority list of things to implement therein.
You may however follow the pre-release development version of standard
RAxML on github.

Alexis

[Karen]

Hi,

a question concerning the automatic Model selection using AUTOF in RAxML Light:

Is it useful to do the tree-Inference with PROTCATAUTOF  (since CAT is faster on the tree inference?)
or is it only useful with PROTGAMMAAUTOF?

If the latter is the case, how can I speed up the tree inference: by doing once a tree inference with PROTGAMMAAUTOF and remaining tree inferences with the selected model?

Karen

[Alexandros Stamatakis]

Hi Karen,

> a question concerning the automatic Model selection using AUTOF in RAxML
> Light:
>
> Is it useful to do the tree-Inference with PROTCATAUTOF (since CAT is
> faster on the tree inference?)
> or is it only useful with PROTGAMMAAUTOF?

I have never properly tested differences between PROTCATAUTOF and
PROTGAMMAAUTOF but I guess/would expect that it should yield the same
model.

You can however test this by running analyses under PROTCATAUTOF and
PROTGAMMAAUTOF on the same starting tree and let us now on here if
different models were selected.

> If the latter is the case, how can I speed up the tree inference: by doing
> once a tree inference with PROTGAMMAAUTOF and remaining tree inferences
> with the selected model?

You can do this by once running AUTOF and then just using the
automatically estimated model for all subsequent analyses.

Alexis

--
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

[Karen]

On Thursday, December 20, 2012 8:08:42 PM UTC+1, Alexis wrote:

Hi Karen,

> a question concerning the automatic Model selection using AUTOF in RAxML
> Light:
>
> Is it useful to do the tree-Inference with PROTCATAUTOF  (since CAT is
> faster on the tree inference?)
> or is it only useful with PROTGAMMAAUTOF?

I have never properly tested differences between PROTCATAUTOF and
PROTGAMMAAUTOF but I guess/would expect that it should yield the same
model.

You can however test this by running analyses under PROTCATAUTOF and
PROTGAMMAAUTOF on the same starting tree and let us now on here if
different models were selected.

okay I will do this and let you know!! (however, I might do this only for one or two starting trees! (I prepared 50 for 50 tree searches) .
I did this once on another data set (5 * GAMMA, 5 * CAT and for this, always the same model was selected).

> If the latter is the case, how can I speed up the tree inference: by doing
> once a tree inference with PROTGAMMAAUTOF and remaining tree inferences
> with the selected model?

You can do this by once running AUTOF and then just using the
automatically estimated model for all subsequent analyses.

okay great :) !!

thanks a lot! karen

[Alexis]

This feature is now available in standard RAxML now as well

Alexis