As in the title: when running a MrBayes analysis on a large (190 samples) SNP dataset, all the 122 trees in the .trprobs file have the same probability (p=0.008). I am looking for the 95% credible set of trees, but I suspect that they should not have the same posterior probability. ESS values are low (200), I still have the same issue.
I did a re-run with higher final ESS values for all parameters (>200) - however, I encountered the same issue: all of the output trees have the same probability.
95% HPD Interval
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Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
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TL 1.061980 0.000095 1.042879 1.080876 1.062098 451.19 601.10 1.001
r(AC) 0.103976 0.000009 0.098559 0.110387 0.103935 281.42 309.01 1.016
r(AG) 0.360533 0.000027 0.350404 0.370181 0.360801 150.72 161.41 1.003
r(AT) 0.071054 0.000006 0.066360 0.075745 0.071203 289.18 321.59 1.001
r(CG) 0.020114 0.000002 0.017775 0.022591 0.020091 317.71 326.55 1.000
r(CT) 0.346303 0.000028 0.336815 0.357066 0.346073 144.77 178.70 1.000
r(GT) 0.098020 0.000008 0.092461 0.103101 0.097997 223.08 252.54 1.000
pi(A) 0.247380 0.000009 0.241770 0.253749 0.247389 263.70 273.91 1.005
pi(C) 0.247447 0.000010 0.242003 0.253900 0.247466 223.47 293.12 1.003
pi(G) 0.254260 0.000009 0.248221 0.259791 0.254200 246.65 248.82 1.005
pi(T) 0.250914 0.000010 0.244960 0.257107 0.250921 260.87 265.54 1.004
alpha 71.419755 35.677437 59.166980 82.053450 71.338790 728.65 739.83 1.001
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Run Arithmetic mean Harmonic mean
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1 -96849.51 -96921.21
2 -96844.91 -96921.99
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TOTAL -96845.59 -96921.67
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Overlay plot shows good plateauing.
Thanks!
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