exclusion of 3rd codon position

[isi]

I was wondering if it is possible in RAxML to exclude 3rd codon
positions of a part of my five-gene-alignment from the analysis? This
would be very helpful and would save much time.....

[Alexis]

Hi Isabella,

There are two options for dealing with 3rd Codon positions:

1. Instead of excluding them, estimating a different model for them,
that is,
estimate distinct model parameters for the 1st and 2nd position
together and the 3rd separately.
You can scroll down at http://wwwkramer.in.tum.de/exelixis/hands-On.html
and look at step 6
to see how this can be specified in the partition file.

2. If you want to exclude sites you can either probably do it with a
tool like mesquite or specify a
RAxML exclude file. In this case you need to run RAxML once with the
exclude file to generate a reduced
alignment and then just do your normal RAxML analysis on that reduced
alignment. This option is described
in the outdated manual at: http://wwwkramer.in.tum.de/exelixis/oldPage/RAxML-Manual.7.0.4.pdf

Hope this helps.

Alexis