Charliep at 17:39, 14 April 2008

2008-04-14T17:39:43Z

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<pre>
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
------------------------------------------------------------------------------
</pre>

Mb-sump-output - Revision history

Charliep at 17:39, 14 April 2008