--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Dec 09 15:11:08 WET 2016
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=CLUSTALW2
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/442/Zasp52-PN/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/442/Zasp52-PN/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/442/Zasp52-PN/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
(Use the harmonic mean for Bayes factor comparisons of models)

(Values are saved to the file /opt/ADOPS/442/Zasp52-PN/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -12569.93        -12583.13
2     -12570.15        -12585.42
--------------------------------------
TOTAL   -12570.03        -12584.83
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/442/Zasp52-PN/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/442/Zasp52-PN/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
Summaries are based on a total of 3002 samples from 2 runs.
Each run produced 2001 samples of which 1501 samples were included.
Parameter summaries saved to file "/opt/ADOPS/442/Zasp52-PN/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.809306    0.001671    0.730200    0.887305    0.808982   1046.78   1200.47    1.000
r(A<->C){all}   0.071754    0.000075    0.055367    0.088986    0.071352   1131.19   1190.34    1.001
r(A<->G){all}   0.254385    0.000300    0.220333    0.288574    0.253785    563.21    674.48    1.000
r(A<->T){all}   0.150031    0.000233    0.118606    0.178097    0.149559    809.74    876.75    1.000
r(C<->G){all}   0.063672    0.000048    0.050608    0.077794    0.063306   1047.57   1140.20    1.000
r(C<->T){all}   0.376616    0.000404    0.337296    0.415402    0.377288    532.41    708.35    1.000
r(G<->T){all}   0.083541    0.000122    0.061664    0.104847    0.082934   1027.81   1083.79    1.000
pi(A){all}      0.236978    0.000042    0.225081    0.249896    0.237257   1121.23   1172.40    1.000
pi(C){all}      0.331427    0.000049    0.317414    0.345170    0.331243   1119.70   1160.86    1.000
pi(G){all}      0.262576    0.000044    0.249869    0.275782    0.262611   1258.76   1312.03    1.000
pi(T){all}      0.169019    0.000029    0.157911    0.178999    0.169048    998.55   1047.69    1.000
alpha{1,2}      0.196306    0.000268    0.164473    0.226990    0.195504   1047.14   1193.71    1.000
alpha{3}        4.012545    0.877975    2.409171    5.928051    3.893311   1487.70   1492.76    1.000
pinvar{all}     0.461109    0.000584    0.415509    0.507535    0.461932   1269.98   1385.49    1.000
------------------------------------------------------------------------------------------------------
* Convergence diagnostic (ESS = Estimated Sample Size); min and avg values
correspond to minimal and average ESS among runs.
ESS value below 100 may indicate that the parameter is undersampled.
+ Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman
and Rubin, 1992) should approach 1.0 as runs converge.


Setting sumt conformat to Simple



 --- CODEML SUMMARY

Model 1: NearlyNeutral	-10684.142614
Model 2: PositiveSelection	-10679.941495
Model 0: one-ratio	-10859.188842
Model 3: discrete	-10669.428685
Model 7: beta	-10676.944448
Model 8: beta&w>1	-10669.85157


Model 0 vs 1	350.0924559999985

Model 2 vs 1	8.402238000002399

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Zasp52-PN)

            Pr(w>1)     post mean +- SE for w

   939 S      0.994**       8.775

Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Zasp52-PN)

            Pr(w>1)     post mean +- SE for w

   254 S      0.511         1.240 +- 0.293
   256 T      0.534         1.253 +- 0.289
   262 T      0.795         1.397 +- 0.202
   386 T      0.565         1.281 +- 0.252
   583 N      0.579         1.282 +- 0.269
   747 A      0.684         1.342 +- 0.233
   830 A      0.661         1.327 +- 0.248
   831 T      0.588         1.287 +- 0.268
   832 V      0.530         1.193 +- 0.404
   834 A      0.510         1.239 +- 0.292
   836 T      0.521         1.244 +- 0.295
   870 F      0.695         1.347 +- 0.231
   884 A      0.648         1.320 +- 0.251
   920 I      0.648         1.324 +- 0.240
   925 L      0.513         1.242 +- 0.290
   939 S      0.934         1.467 +- 0.125
   943 K      0.558         1.270 +- 0.276
   945 T      0.603         1.296 +- 0.263
   948 F      0.542         1.261 +- 0.277
   990 P      0.503         1.161 +- 0.432
   993 G      0.745         1.373 +- 0.219


Model 8 vs 7	14.185755999998946

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Zasp52-PN)

            Pr(w>1)     post mean +- SE for w

   262 T      0.767         5.616
   939 S      1.000**       7.128

Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Zasp52-PN)

            Pr(w>1)     post mean +- SE for w

   251 P      0.553         1.003 +- 0.578
   254 S      0.645         1.145 +- 0.497
   256 T      0.680         1.181 +- 0.482
   262 T      0.967*        1.473 +- 0.150
   386 T      0.773         1.289 +- 0.400
   451 S      0.584         1.079 +- 0.519
   460 R      0.506         0.946 +- 0.588
   583 N      0.760         1.268 +- 0.427
   626 G      0.514         0.954 +- 0.588
   737 S      0.513         0.954 +- 0.587
   738 K      0.587         1.085 +- 0.514
   747 A      0.919         1.432 +- 0.235
   825 I      0.575         1.029 +- 0.571
   830 A      0.864         1.373 +- 0.329
   831 T      0.773         1.281 +- 0.418
   832 V      0.645         1.113 +- 0.542
   834 A      0.644         1.144 +- 0.497
   836 T      0.650         1.147 +- 0.498
   870 F      0.913         1.424 +- 0.252
   880 A      0.548         0.996 +- 0.579
   882 A      0.554         1.006 +- 0.575
   884 A      0.850         1.359 +- 0.346
   886 A      0.576         1.031 +- 0.571
   920 I      0.874         1.388 +- 0.304
   925 L      0.651         1.152 +- 0.493
   939 S      0.997**       1.498 +- 0.041
   943 K      0.728         1.234 +- 0.451
   945 T      0.796         1.305 +- 0.399
   947 P      0.540         0.987 +- 0.581
   948 F      0.709         1.216 +- 0.459
   990 P      0.601         1.060 +- 0.563
   993 G      0.943         1.452 +- 0.202