how to select JTT+I+G+F in RAxML version 8.0.0

[harnv]

Hello everybody,

I have got the best model, which is JTT+I+G+F, based on the result form Protest .

However, I am not sure that I use the correct command in RAxML version 8.0.0.

I greatly appreciate if someone can comment from this followed.

./raxml -m PROTGAMMAIJTTF -s input -n output -T 2 -f a -p 15000 -x 16000 -#1000

Another additional question is what's the value of -T -x and -p that we should use for analysis?

Thank you so much,

harn

[Alexandros Stamatakis]

On 22.03.2017 16:53, harnv wrote:
> Hello everybody,
>
> I have got the best model, which is JTT+I+G+F, based on the result form
> Protest .
> However, I am not sure that I use the correct command in RAxML version
> 8.0.0.
> I greatly appreciate if someone can comment from this followed.
>
> ./raxml -m PROTGAMMAIJTTF -s input -n output -T 2 -f a -p 15000 -x 16000
> -#1000

that's correct, but you should urgently update to either RAxML-NG (the
new complete re-design of RAxML) or at least to RAxML v 8.2.10

> Another additional question is what's the value of -T

please see previous discussions on setting an appropriate number of
Threads for the PThreads version of RAxML, if you are actually using it,
rather looks as if you are using the sequential version.

> -x and -p that we
> should use for analysis?

any random integer values, those are random number seeds!

alexis

>
>
> Thank you so much,
>
> harn
>
>

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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