Hi!
I'm doing a phylogenetic reconstruction in mrbayes, and I think that maybe there's something wrong with my script, because I asked for a 25% generations burn-in, but when I look at the run.p in Tracer, it seems to take just 10%. Here they go the script and a screenshot of tracer:
#NEXUS
begin mrbayes;
begin data;
dimensions ntax=105 nchar=1121;
FORMAT DATATYPE=DNA MISSING=? GAP=- MATCHCHAR=.;
MATRIX
(sequences)
;
end;
Lset nst=2 rates=invgamma;
mcmcp ngen=1000000 printfreq=100 samplefreq=100 nchains=4 savebrlens=yes burninfrac=0.25
filename=sinmiss;
end;
Is there sth I'm doing wrong? Thanks in advance!
Andrii Tarieiev
You can try to add the following line to your script:
sump relburnin=yes burninfrac=0.25
Then, you will be able to see the summary in Tracer.
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