codon models in RAxML

[Karen]

Hi to all,
is there any plan to implement also codon models in RAxML?
Karen

[Alexis]

not any time soon I am afraid, but GARLI can do Codon models.

If I remember correctly Derrick Zwickl had found that his Codon model
implementation in GARLI did not yield
different trees than conducting searches under simpler (less memory
and compute-intensive) DNA and/or protein models.

Hence, my reluctance to spend/waste time for implementing Codon models
in RAxML.
However, the codon stuff may be useful for post-analyses given a fixed
tree.

Alexis

[Heiko]

On Aug 21, 6:10 pm, Karen <kmeusem...@googlemail.com> wrote:
> is there any plan to implement also codon models in RAxML?

If you really want to do ML with codons you could think about using
IQPNNI as that one allows codon models in the tree search (http://
www.cibiv.at/software/iqpnni).

Alexis - I hope this suggestion is OK on this list, since RAxML does
not implement codon models 8)

Best wishes,
Heiko

[Alexis]

I don't mind at all, we are here to help people analyze there data,

Alexis

[JK]

I just thought I'd bump this thread - any news on implementing mechanistic or empirical codon models in RAxML? I know that they are all quite a pain to run in terms of time-cost, but the excellent parallelization of RAxML seems to me perfectly suited to handle it. Just curious, is all...

Cheers,
-Jacek

[Alexandros Stamatakis]

Hi Jacek,

it's on the list, but will still take some time,

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