Hello,
I am stacked in the nexus file for a combined data analysis on mrbayes It is not working and don"t know where is the mistake .... in the header or rather in the endblock ...
that's the content
#NEXUS
BEGIN DATA;
dimensions ntax=50 nchar=638;
format missing=?
interleave=yes datatype=mixed(DNA:1-627, Standard:628-638) gap=- match=.;
matrix
begin mrbayes;
outgroup S_long, S_minus, S_bail;
charset 28S = 1-627;
charset morphology = 628-638;
partition favored = 2: 28S, morphology;
set partition = favored;
lset applyto=(1) nst=2 rates=invgamma;
lset applyto=(2) rates=gamma;
unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all);
prset applyto=(all) ratepr=variable;
mcmcp ngen=100000 samplefreq=100 nchains=4;
end;
many thank's for your consideration I hope somebody can help me
How far does it get? MrBayes will read the information and stop the process at the point where it hits an error, so that is usually a good place to start troubleshooting. What is the last command that MrBayes successfully reads before it stops? My understanding was that only a single outgroup taxon could be used. You can always reroot the tree later. If it reads the whole file, but doesn't start to run then that's because 'mcmp' doesn't actually start the chain, 'mcmc' does.
I may be missing something. But don't you need the line: execute [file].nex; after the begin mrbayes; line?
what is the message you get? Do you have your data file in a folder where MrBayes can find it (usually your home folder).
hello
many thank's for your answers I corrected my nexus file according to you ideas and I worked ..
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