--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Dec 11 21:35:32 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_S3_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Pint_S3_17/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_S3_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -13892.08 -13917.01
2 -13892.03 -13912.22
--------------------------------------
TOTAL -13892.06 -13916.32
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/pet1/Pint_S3_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Pint_S3_17/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_S3_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 3.627405 0.013296 3.414461 3.857974 3.624874 1282.48 1363.12 1.000
r(A<->C){all} 0.128117 0.000091 0.110577 0.146800 0.127866 887.21 953.55 1.000
r(A<->G){all} 0.296704 0.000209 0.269182 0.325626 0.296791 662.49 670.84 1.002
r(A<->T){all} 0.092991 0.000043 0.079519 0.104516 0.092893 838.43 897.43 1.000
r(C<->G){all} 0.137858 0.000125 0.117557 0.160356 0.137439 837.38 905.78 1.000
r(C<->T){all} 0.262408 0.000178 0.235917 0.288525 0.262436 745.19 759.68 1.003
r(G<->T){all} 0.081922 0.000050 0.068487 0.095028 0.081634 983.71 997.62 1.000
pi(A){all} 0.311280 0.000090 0.291905 0.329012 0.311227 698.63 820.41 1.000
pi(C){all} 0.175507 0.000053 0.162181 0.189778 0.175307 605.52 675.52 1.000
pi(G){all} 0.188069 0.000064 0.172498 0.203645 0.188037 924.15 943.31 1.000
pi(T){all} 0.325144 0.000093 0.307347 0.344518 0.324877 712.01 843.28 1.000
alpha{1,2} 1.288866 0.025535 1.008151 1.602495 1.275239 1001.42 1104.21 1.000
alpha{3} 4.272607 0.705589 2.831418 5.992226 4.193261 1274.41 1387.71 1.000
pinvar{all} 0.050411 0.000394 0.014214 0.091680 0.050282 1090.03 1124.99 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 -12109.745604
Model 2: PositiveSelection -12098.02715
Model 0: one-ratio -12316.80654
Model 3: discrete -12056.30451
Model 7: beta -12079.892778
Model 8: beta&w>1 -12051.490486
Model 0 vs 1 414.1218719999997
Model 2 vs 1 23.436907999999676
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_S3_A113_AY363972_AAR15913)
Pr(w>1) post mean +- SE for w
50 V 0.795 2.086
64 Y 0.860 2.175
66 F 0.965* 2.319
97 S 0.650 1.889
100 V 0.562 1.768
117 S 0.966* 2.321
118 L 0.919 2.256
149 S 0.596 1.815
179 M 0.634 1.867
199 I 0.962* 2.315
202 W 0.776 2.061
218 F 0.858 2.173
219 A 0.906 2.239
241 G 0.562 1.768
263 P 0.733 2.002
264 S 0.541 1.739
336 T 0.874 2.195
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_S3_A113_AY363972_AAR15913)
Pr(w>1) post mean +- SE for w
50 V 0.779 2.172 +- 0.628
64 Y 0.859 2.293 +- 0.530
66 F 0.964* 2.452 +- 0.291
97 S 0.624 1.939 +- 0.730
100 V 0.530 1.797 +- 0.752
117 S 0.969* 2.459 +- 0.275
118 L 0.918 2.382 +- 0.421
149 S 0.557 1.837 +- 0.747
179 M 0.603 1.906 +- 0.737
199 I 0.965* 2.453 +- 0.290
202 W 0.753 2.132 +- 0.651
218 F 0.850 2.280 +- 0.542
219 A 0.901 2.357 +- 0.456
241 G 0.520 1.781 +- 0.751
263 P 0.716 2.077 +- 0.681
264 S 0.502 1.753 +- 0.752
336 T 0.865 2.302 +- 0.519
Model 8 vs 7 56.8045839999977
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_S3_A113_AY363972_AAR15913)
Pr(w>1) post mean +- SE for w
50 V 0.966* 1.846
64 Y 0.968* 1.847
66 F 0.995** 1.879
97 S 0.933 1.809
100 V 0.907 1.779
117 S 0.994** 1.877
118 L 0.987* 1.870
149 S 0.922 1.796
176 D 0.777 1.630
179 M 0.915 1.788
199 I 0.992** 1.875
202 W 0.962* 1.841
218 F 0.980* 1.861
219 A 0.987* 1.869
241 G 0.905 1.776
263 P 0.947 1.824
264 S 0.898 1.770
336 T 0.982* 1.864
349 L 0.744 1.591
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_S3_A113_AY363972_AAR15913)
Pr(w>1) post mean +- SE for w
50 V 0.923 2.249 +- 0.523
64 Y 0.945 2.287 +- 0.480
66 F 0.989* 2.350 +- 0.372
97 S 0.847 2.129 +- 0.637
100 V 0.785 2.028 +- 0.704
117 S 0.990* 2.352 +- 0.370
118 L 0.976* 2.331 +- 0.409
149 S 0.793 2.040 +- 0.695
176 D 0.526 1.600 +- 0.815
179 M 0.801 2.054 +- 0.692
199 I 0.987* 2.348 +- 0.378
202 W 0.904 2.218 +- 0.557
218 F 0.955* 2.299 +- 0.458
219 A 0.971* 2.323 +- 0.420
241 G 0.749 1.968 +- 0.734
263 P 0.887 2.194 +- 0.584
264 S 0.741 1.955 +- 0.738
336 T 0.958* 2.304 +- 0.450
