bethnon.mb

begin mrbayes;
[Script documentation carried out using comments]

[log the analysis]
log start filename=bethnon.log;
[read the matrix bethnon.aligned.fasta.nexus.std]
execute bethnon.aligned.fasta.nexus.std;

[close analysis at end]
set autoclose=yes;
[This command shows the status of all the taxa, according to the documentation]
taxastat;

[definition of individual partitions per marker]
charset morph=1-139;

[definition of the single partition]
partition chants=1:morph;

[specification of substitution models]
set partition=chants;
lset applyto=(1) coding=all rates=invgamma; [Mkv+I+G, nstates is automatic for the standard datatype]

[show the model just specified for each partition]
showmodel;

[set up the MCMC, with this setting the analysis will need not less than 16 threads]
mcmcp nruns=4 ngen=10000000 nchains=4 samplefreq=1000 printfreq=1000;
[run the MCMC]
mcmc;

[summarize the posterior trees]
sumt nruns=4 relburnin=yes burninfrac=0.50;
plot;

[summarize parameter posteriors]
sump;

log stop;
end;