Question: Testing a force topology in mrBayes
4.5 years ago by
Reema Singh • 150
Reema Singh • 150 wrote:
Hello Everybody, I have a question related to "Testing a topological hypothesis". I have tried to run the same procedure as mentioned in the tutorial in order to check whether two species form monophyletic group or not. As far as i understand the manual- - by setting hard constraint we are forcing two species to form a monophyletic group every time. And by setting the negative constraint we should reproduce the original topology. However, In my case , after running the analysis as mentioned in the manual- both hard and negative constraint are producing the same tree. After running the stepping stone analysis, i am getting some weird output in log file:- "24600 -- [nan] (nan) (nan) (nan) * [nan] (nan) (nan) (nan) (...0 remote chains" Run Marginal likelihood (ln) ------------------------------ 1 nan 2 nan ------------------------------ Mean: nan As I am running the entire analysis on the cluster. So, here's the command i am using for this analysis:- "begin mrbayes; set autoclose=yes nowarn=yes; execute Set1_Out_Ehist_Concat.nexus; lset rates=invgamma; constraint subell = Asub Aell; constraint nosubell = Asub Aell; prset topologypr = constraints(subell); mcmc ngen=100000 samplefreq=100 printfreq=100 diagnfreq=1000 file=PositiveConstraint; sump burnin=25000; sumt burnin=25000; prset topologypr = constraints(nosubell); mcmc ngen=100000 samplefreq=100 printfreq=100 diagnfreq=1000 file=NegativeConstraint; sump burnin=25000; sumt burnin=25000; prset topologypr = constraints(subell); ss ngen=250000 diagnfreq=2500 filename=positive; prset topologypr = constraints(nosubell); ss filename=negative; quit; end; " Here the Asub and Aell are the two species name that i want to be force to form a monophyletic group in the hard constraint. Now I don't understand what is happening here. And my questions are :- 1) Why i am getting the same tree after setting hard and negative constraint? 2) What does this "*nan"* mean in the stepping stone analysis? 3) How do i known if the procedure i am running is correct or not? As these question making me very confuse now. So I would highly appreciate any help and clarification on this questions. I have also posted this question on the mrbayes mailing list[http://sourceforge.net/p/mrbayes/mailman/message/34174009/], but i didn't get any reply.
Looking forward for the answer.
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