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Old 06-09-2015, 02:56 PM   #1
reema
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Location: Scotland

Join Date: Feb 2014
Posts: 27
Default Testing a force topology in mrBayes

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/mai...age/34174009/] as well as biostar[https://www.biostars.org/p/145595/], but i didn't get any reply.

Very much looking forward for the answer
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evolutionary analysis, phylogenetic analysis

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