Mb-sump-output

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MrBayes > sump filename=Testudinoidea_all-1.nex.mb nruns=1

   Setting sump filename to Testudinoidea_all-1.nex.mb
   Setting sump output file to Testudinoidea_all-1.nex.mb.stat
   Setting sump nruns to 1
   Summarizing parameters in file Testudinoidea_all-1.nex.mb.p
   Writing output to screen but not to file ('Printtofile = No')
   UNIX line termination
   Longest line length = 124
   Found 5001 parameter lines in file "Testudinoidea_all-1.nex.mb"
   All 5001 lines will be summarized (starting at line 3)
   (Only the last set of lines will be read, in case multiple
   parameter blocks are present in the same file.)
   5001 rows and 14 columns in each row
   Successfully read 5001 lines from last parameter block

   Below is a rough plot of the generation (x-axis) versus the log   
   probability of observing the data (y-axis). You can use this      
   graph to determine what the burn in for your analysis should be.  
   When the log probability starts to plateau you may be at station- 
   arity. Sample trees and parameters after the log probability      
   plateaus. Of course, this is not a guarantee that you are at sta- 
   analysis should be. When the log probability starts to plateau    
   tionarity. When possible, run multiple analyses starting from dif-
   ferent random trees; if the inferences you make for independent   
   analyses are the same, this is reasonable evidence that the chains
   have converged. You can use MrBayes to run several independent    
   analyses simultaneously. During such a run, MrBayes will monitor  
   the convergence of topologies. After the run has been completed,  
   the 'sumt' and 'sump' functions will provide additional conver-   
   gence diagnostics for all the parameters in your model. Remember  
   that the burn in is the number of samples to discard. There are   
   a total of ngen / samplefreq samples taken during a MCMC analysis.

   +------------------------------------------------------------+ -50896.09
   | ***********************************************************|
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   |*                                                           |
   +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ -52237.00
   ^                                                            ^
   1                                                            5000000


   Estimated marginal likelihoods for run sampled in file "Testudinoidea_all-1.nex.mb.p":
      (Use the harmonic mean for Bayes factor comparisons of models)

   Arithmetic mean   Harmonic mean
   --------------------------------
      -50878.70 *       -87193.62 *
   --------------------------------
   * These estimates may be unreliable because 
     some extreme values were excluded


   Model parameter summaries for run sampled in file "Testudinoidea_all-1.nex.mb":
      (Based on a total of 5001 samples out of a total of 5001 samples from this analysis)

                                              95% Cred. Interval
                                            ----------------------
   Parameter       Mean        Variance       Lower         Upper         Median
   ------------------------------------------------------------------------------
   TL            5.363889      0.364596      5.104000      5.576000      5.328000
   r(A<->C)      0.052355      0.000010      0.047490      0.057619      0.052272
   r(A<->G)      0.224344      0.000102      0.206142      0.243204      0.224514
   r(A<->T)      0.053276      0.000011      0.047998      0.059155      0.053220
   r(C<->G)      0.017005      0.000007      0.013740      0.020402      0.016936
   r(C<->T)      0.629575      0.000189      0.609984      0.650019      0.629242
   r(G<->T)      0.023446      0.000011      0.018576      0.028516      0.023368
   pi(A)         0.329686      0.000039      0.317861      0.342043      0.329402
   pi(C)         0.278162      0.000031      0.268185      0.288695      0.278227
   pi(G)         0.171375      0.000031      0.160837      0.181418      0.171369
   pi(T)         0.220777      0.000023      0.211556      0.229830      0.220873
   alpha         0.229991      0.000050      0.218927      0.241060      0.229703
   ------------------------------------------------------------------------------
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