Dear Sergei,
I seem to be having similar strange results with
nonparametric
bootstrap estimates using simpleBootstrap.bf. However, for the same dataset the
parametric
means and variances seem reasonable. Below are some of the summary values that seem strange from the nonparametric bootstraps.
+-------------------------------------------------------------------------------
-------------+
| Parameter | MLE | Mean | Variance |
+-------------------------------------------------------------------------------
-------------+
| AC | 0.680938 | 26.357789 | 18220.0152105 |
| AT | 0.106453 | 101.102172 | 999795.7313688 |
| givenTree.Node114.nonSynRate | 0.517753 | 332.868276 | 2954236.9980986 |
| givenTree.Node114.synRate | 1.072250 | 47.574958 | 135608.0128181 |
Ln-Lklhood |-21483.516754 | -34435.874822 | 29173030835.8369141
I am using the simpleBootstrap.bf that comes with 0.99beta and is identical to 1.00beta. I have modified the script to write the summary to a file and I have hardwired some of the #includes and ExecuteAFile arguments, but I don't see anything I changed that could have effected the results. Again, the parametric bootstraps seemed fine with the same script. I was using the MPI version. I am using the same tree and dataset that I sent you a few days ago. Before I try to debug this myself I was hoping the difference in behaviour between the parametric and nonparametric might give you a clue to what could be happening. Below are links to my slightly modified simpleBootstrap.bf and the nonparametric results.
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p.s. I haven't been able to connect to Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
for several days.