few warning while using PROTGAMMAIJTTF as model

[Reetu Tuteja]

Dear RAxML Team,

I am a beginner in phylogenetics and using RAxML for the first time.

I got JTT+I+G+F as the best model using modelgenerator. Is this correct to use -m PROTGAMMAIJTTF option in RAxML?

When I used this model in my command I got the following warning:

You are using a proportion of Invariable sites estimate, although I don't
like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001
to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar

What should I do? Please help.

Thanks,
Reetu

[Andre J. Aberer]

Hi Reetu,

> I am a beginner in phylogenetics and using RAxML for the first time.
>
> I got JTT+I+G+F as the best model using modelgenerator. Is this correct to use -m PROTGAMMAIJTTF option in RAxML?
>

Yes, as an alternative you can use PROTCATIJTTF as well (CAT
approximates GAMMA, is faster and yields comparable trees).

>
> When I used this model in my command I got the following warning:
>
> You are using a proportion of Invariable sites estimate, although I don't
> like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001
> to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar
>
> What should I do? Please help.

Just drop the "I" (PROTGAMMAJTTF). Somewhen, Alexis gave the reason in
this group, why "invariable sites" (that's what the "I" stands for) can
be problematic (maybe just google for it, if you want to go deeper into
it).

--
Best regards,
Andre J. Aberer

M.Sc. (Bioinformatics)
Scientific Computing Group

Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Schloss-Wolfsbrunnenweg 35
D-69118 Heidelberg

Tel.: +49 6221 533 264
Fax: +49 6221 533 298
WWW: http://www.exelixis-lab.org
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Amtgericht Mannheim / HRB 337446
Managing Directors: Dr. h.c. Dr.-Ing. E.h. Klaus Tschira, Prof. Dr.-Ing. Andreas Reuter

[Alexandros Stamatakis]

Hi Reetu,

Please have a look at page 20/21 of the RAxML v 704 manual
http://sco.h-its.org/exelixis/oldPage/RAxML-Manual.7.0.4.pdf

where I explain the reasons why GAMMA+P-Invar should not be used
together.

Alexis

On Sun, 2012-09-23 at 21:54 +0200, Andre J. Aberer wrote:
> Hi Reetu,
>
> > I am a beginner in phylogenetics and using RAxML for the first time.
> >
> > I got JTT+I+G+F as the best model using modelgenerator. Is this correct to use -m PROTGAMMAIJTTF option in RAxML?
> >
>
> Yes, as an alternative you can use PROTCATIJTTF as well (CAT
> approximates GAMMA, is faster and yields comparable trees).
>
> >
> > When I used this model in my command I got the following warning:
> >
> > You are using a proportion of Invariable sites estimate, although I don't
> > like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001
> > to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar
> >
> > What should I do? Please help.
>
> Just drop the "I" (PROTGAMMAJTTF). Somewhen, Alexis gave the reason in
> this group, why "invariable sites" (that's what the "I" stands for) can
> be problematic (maybe just google for it, if you want to go deeper into
> it).
>

--

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

[sam shaunessy]

Hi, i was wondering if someone could help me. I'm trying to thoroughly understand the RAxML algorithm in laymens terms, and how it differs/betters from PhyML/MrBayes ( i am not familiar with bioinformatics, but struggling to be!)

I found this..

http://bioinformatics.oxfordjournals.org/content/21/4/456.full.pdf

Is it...

1. An initial tree is suggested with NJ (so this is you have an alignment, you make a distance matrix and then a NJ from this).

2. For an alignment, the likelihood of the tree is calculated (for each site in the alignment, you ask what's the probability of seeing that site, given the tree. Then you sum the site likelihoods to get a tree likelihood).

3. You change the tree, with SPR. this takes chunks of the tree and attaches them elsewhere.

4. If the new tree has a better likelihood, it is the new most likely tree.

5. This step is repeated over until no better tree is found.

...and finally, it is faster than PhyML/MyBayes?

Many thanks

Sam.

[Alexandros Stamatakis]

Dear Sam,

I believe that it would be better if you started by reading the standard
textbooks by Ziheng Yang and Joe Felsenstein.

And please do not post questions like these under unrelated topics.

Cheers,

Alexis

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