--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Dec 11 20:40:17 WET 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
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=
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/pet1/Pint_S2_18/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Pint_S2_18/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/ADOPS1/pet1/Pint_S2_18/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -13918.63 -13936.78
2 -13918.26 -13939.14
--------------------------------------
TOTAL -13918.43 -13938.54
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/pet1/Pint_S2_18/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Pint_S2_18/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/ADOPS1/pet1/Pint_S2_18/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 3.570211 0.012689 3.368393 3.803866 3.569041 1360.86 1409.50 1.000
r(A<->C){all} 0.139298 0.000092 0.121598 0.158565 0.139008 916.72 971.10 1.000
r(A<->G){all} 0.290620 0.000206 0.263918 0.319490 0.290629 604.78 696.29 1.000
r(A<->T){all} 0.094491 0.000044 0.081542 0.107068 0.094480 813.06 933.03 1.000
r(C<->G){all} 0.129154 0.000114 0.109524 0.149503 0.129191 766.38 863.05 1.000
r(C<->T){all} 0.263421 0.000181 0.237060 0.288683 0.263255 545.28 643.45 1.000
r(G<->T){all} 0.083016 0.000050 0.070393 0.097245 0.082843 888.20 976.98 1.000
pi(A){all} 0.306458 0.000091 0.287932 0.324752 0.306388 775.56 794.61 1.000
pi(C){all} 0.171001 0.000053 0.155664 0.184053 0.171047 737.60 773.60 1.000
pi(G){all} 0.193716 0.000062 0.177350 0.208718 0.193738 823.29 879.81 1.000
pi(T){all} 0.328825 0.000096 0.309163 0.347407 0.328699 565.76 637.07 1.000
alpha{1,2} 1.239160 0.019391 0.993806 1.518003 1.227882 1301.00 1350.92 1.000
alpha{3} 3.709573 0.485505 2.485051 5.106282 3.630189 1101.27 1237.99 1.000
pinvar{all} 0.029534 0.000310 0.000008 0.060092 0.028140 1165.11 1239.22 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 -12137.870925
Model 2: PositiveSelection -12131.258328
Model 0: one-ratio -12335.13171
Model 3: discrete -12087.832599
Model 7: beta -12110.330321
Model 8: beta&w>1 -12087.784215
Model 0 vs 1 394.5215700000008
Model 2 vs 1 13.225193999998737
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 1_Pintegrifolia_S2_A113_AY363971_AAR15912)
Pr(w>1) post mean +- SE for w
50 V 0.877 2.043
64 Y 0.882 2.050
66 F 0.958* 2.141
95 S 0.517 1.615
115 S 0.934 2.112
116 L 0.862 2.027
200 W 0.607 1.723
216 F 0.538 1.640
217 A 0.593 1.706
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: 1_Pintegrifolia_S2_A113_AY363971_AAR15912)
Pr(w>1) post mean +- SE for w
50 V 0.890 2.297 +- 0.520
64 Y 0.902 2.317 +- 0.501
66 F 0.961* 2.398 +- 0.387
95 S 0.506 1.728 +- 0.745
115 S 0.945 2.379 +- 0.420
116 L 0.878 2.281 +- 0.537
197 I 0.509 1.738 +- 0.749
200 W 0.581 1.835 +- 0.737
216 F 0.518 1.743 +- 0.744
217 A 0.572 1.822 +- 0.740
Model 8 vs 7 45.09221199999956
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 1_Pintegrifolia_S2_A113_AY363971_AAR15912)
Pr(w>1) post mean +- SE for w
50 V 0.989* 1.605
64 Y 0.987* 1.603
66 F 0.997** 1.612
95 S 0.943 1.565
98 V 0.594 1.247
115 S 0.993** 1.608
116 L 0.988* 1.604
147 S 0.931 1.554
157 V 0.728 1.368
173 C 0.510 1.170
174 D 0.832 1.464
177 M 0.869 1.497
197 I 0.905 1.530
200 W 0.959* 1.578
216 F 0.955* 1.575
217 A 0.962* 1.581
241 G 0.708 1.349
262 M 0.847 1.478
263 P 0.647 1.292
264 S 0.776 1.413
267 T 0.664 1.311
311 S 0.834 1.466
315 H 0.835 1.469
336 T 0.938 1.560
349 P 0.701 1.343
353 S 0.898 1.524
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: 1_Pintegrifolia_S2_A113_AY363971_AAR15912)
Pr(w>1) post mean +- SE for w
50 V 0.947 1.487 +- 0.209
64 Y 0.938 1.480 +- 0.220
66 F 0.978* 1.508 +- 0.174
95 S 0.825 1.399 +- 0.299
115 S 0.961* 1.496 +- 0.195
116 L 0.941 1.483 +- 0.216
147 S 0.801 1.380 +- 0.310
157 V 0.524 1.162 +- 0.385
174 D 0.644 1.258 +- 0.366
177 M 0.698 1.299 +- 0.357
197 I 0.754 1.345 +- 0.340
200 W 0.861 1.425 +- 0.277
216 F 0.849 1.417 +- 0.281
217 A 0.867 1.430 +- 0.272
241 G 0.505 1.144 +- 0.384
262 M 0.663 1.273 +- 0.359
264 S 0.575 1.203 +- 0.376
311 S 0.646 1.259 +- 0.361
315 H 0.644 1.262 +- 0.355
336 T 0.815 1.391 +- 0.303
353 S 0.741 1.333 +- 0.332
