Question: Testing a force topology in mrBayes
0
gravatar for Reema Singh
4.5 years ago by
Reema Singh150
United Kingdom
Reema Singh150 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.

Many Thanks,
Reema Singh,

ADD COMMENTlink modified 7 months ago by 17th Level Botanist30 • written 4.5 years ago by Reema Singh150
0
gravatar for 17th Level Botanist
7 months ago by
17th Level Botanist30 wrote:

For Q1:

It looks to me like you set the exact same constraint twice. I think you need to revise

constraint nosubell = Asub Aell;

to

constraint nosubell negative = Asub Aell;

The default constraint is hard, which is why you do not need to specify that one.

ADD COMMENTlink modified 7 months ago • written 7 months ago by 17th Level Botanist30
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