BINCAT without rate heterogeneity

[Antony Vincent]

Hello,

I want to perform a phylogeny using a binary-encoded matrix. When I executed RAxML, I received this output:

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!

I tried with the following command line:
raxmlHPC-PTHREADS-AVX -m BINCAT -s binary_matrix.fasta -V -p 12345 -n propre -T 10

and I still received the same output.

Is the -V option works with a binary matrix?

Thank you!

[Alexandros Stamatakis]

you still get the warning because model parameters and br-lens of the
final tree will still be estimated under GAMMA, this is nothing to worry
about, since a high alpha parameter does not mean that you should not
use Gamma, but rather that you don't need to use GAMMA which will make
the likelihood computations during the tree search execute faster,

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 answer!