Dear Karen,
> is the number of partitions in RAxML-7.2.8-ALPHA limited?
yes it's limited to 128
> I have a
> dataset with more than 150 partitions and would like to conduct a
> partitioned analysis on a superalignment (multiple genes on aa level).
> If the number is limited, is there an option to change this?
I wouldn't call this an option, but there is a way to change this.
Edit the following line in source file axml.h
#define NUM_BRANCHES 128
to read
#define NUM_BRANCHES 128
then, just re-compile the program.
Don't forget to remove all object files by typing "rm *.o" first
before you re-compile.
> Furthermore I wonder if a partitioned analysis with different models
> (estimated e.g. by ProtTest) for each partition (aa level, 50-300
> sites) might be useful or not - maybe they are too short for a proper
> model estimation?
It may make sense to do this, since your trees don't have that many
taxa.
In fact on my software page at
www.exelixis-lab.org/software.html if
you scroll down
there is a perl script to do this, i.e., split up the alignment into
per-gene alignments, build a parsimony tree
for each of them, and then just compute the likelihood on the fixed
tree for all available models and keep the best one.
Cheers,
Alexis