Phylogeny based on presence/absence of genes

[Antony Vincent]

Hi,

I want to perform of phylogeny based on a matrix composed of discrete character data with two states (0 and 1), corresponding at the presence/absence of genes. I used RAxML version 8.2.4 with the model BINGAMMA. RAxML gave me a warning:

WARNING the alpha parameter with a value of 1000.000000 estimated by RAxML for partition number 0 with the name "No Name Provided"

is larger than 10.000000. You should do a model test and confirm that you actually need to incorporate a model of rate heterogeneity!

You can run inferences with a plain substitution model (without rate heterogeneity) by specifyng the CAT model and the "-V" option!

However, the manual says:

Warning: It is not a good idea to use the CAT approximation of rate heterogeneity on datasets with less than 50 taxa. In general there will not be enough data per alignment column available to reliably estimate the per-site rate parameters.

The problem is that I have 19 taxa. Do you have any advice?

Thank you!

Antony

[Alexandros Stamatakis]

the -V option disables the per-site rates option, or to be more precise
only allows for one single rate category for all sites which is set to
1.0, thus -m GTRCAT in combination with -V yields a plain GTR
substitution model without rate heterogeneity ...

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

[Antony Vincent]

Thank you for the quick answer.

In my case, since I want to use a binary matrix (0 and 1), I suppose I should use -m BINCAT -V. Is it this?

Antony

[Alexandros Stamatakis]

yes that's right,

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 <http://www.exelixis-lab.org>

[Antony Vincent]

Thank you again :-)

Antony