--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Dec 11 19:42:36 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/Phyb_S9_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Phyb_S9_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/Phyb_S9_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -13553.48 -13576.93
2 -13553.43 -13571.51
--------------------------------------
TOTAL -13553.45 -13576.24
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/pet1/Phyb_S9_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Phyb_S9_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/Phyb_S9_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} 3.536690 0.013201 3.333604 3.776635 3.535394 1188.44 1268.09 1.000
r(A<->C){all} 0.130121 0.000098 0.110287 0.148823 0.130163 643.71 728.57 1.000
r(A<->G){all} 0.297451 0.000216 0.268393 0.326134 0.297276 569.10 627.66 1.000
r(A<->T){all} 0.096743 0.000047 0.083642 0.110140 0.096715 768.33 838.26 1.001
r(C<->G){all} 0.133463 0.000122 0.112153 0.155395 0.133059 848.60 883.45 1.000
r(C<->T){all} 0.250415 0.000176 0.225188 0.276768 0.249969 507.01 594.36 1.002
r(G<->T){all} 0.091808 0.000059 0.075975 0.106083 0.091483 922.61 946.85 1.000
pi(A){all} 0.307904 0.000092 0.290312 0.327835 0.307744 475.61 546.70 1.005
pi(C){all} 0.173179 0.000053 0.158840 0.186723 0.173187 750.01 765.24 1.002
pi(G){all} 0.196788 0.000062 0.182462 0.212541 0.196674 715.70 854.60 1.000
pi(T){all} 0.322128 0.000093 0.304549 0.341947 0.322047 730.52 745.04 1.002
alpha{1,2} 1.330122 0.031922 1.018504 1.688174 1.314665 1241.02 1243.59 1.001
alpha{3} 4.324738 0.688205 2.696392 5.889682 4.249835 1184.07 1253.16 1.000
pinvar{all} 0.061553 0.000432 0.021973 0.103294 0.061963 1047.03 1060.28 1.002
------------------------------------------------------------------------------------------------------
* 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 -11816.21765
Model 2: PositiveSelection -11803.58689
Model 0: one-ratio -12018.735836
Model 3: discrete -11752.851614
Model 7: beta -11781.82906
Model 8: beta&w>1 -11754.698045
Model 0 vs 1 405.03637199999866
Model 2 vs 1 25.26152000000002
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_Phybrida_S9_FBX1_AB933000)
Pr(w>1) post mean +- SE for w
51 T 0.887 2.348
65 S 0.767 2.166
67 R 0.991** 2.506
97 C 0.889 2.352
117 Y 0.921 2.401
118 V 0.844 2.283
149 Q 0.903 2.372
218 E 0.916 2.392
219 P 0.964* 2.466
243 F 0.920 2.398
338 K 0.536 1.816
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_Phybrida_S9_FBX1_AB933000)
Pr(w>1) post mean +- SE for w
51 T 0.885 2.386 +- 0.552
65 S 0.768 2.204 +- 0.698
67 R 0.991** 2.552 +- 0.295
97 C 0.887 2.388 +- 0.548
117 Y 0.921 2.444 +- 0.488
118 V 0.842 2.317 +- 0.614
149 Q 0.899 2.406 +- 0.525
218 E 0.913 2.427 +- 0.501
219 P 0.963* 2.507 +- 0.386
243 F 0.919 2.440 +- 0.492
338 K 0.533 1.822 +- 0.783
Model 8 vs 7 54.26203000000169
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_Phybrida_S9_FBX1_AB933000)
Pr(w>1) post mean +- SE for w
30 V 0.695 1.541
51 T 0.982* 1.865
65 S 0.953* 1.832
67 R 0.998** 1.882
97 C 0.986* 1.868
117 Y 0.985* 1.868
118 V 0.975* 1.856
142 E 0.506 1.317
149 Q 0.988* 1.871
178 L 0.661 1.501
199 T 0.712 1.558
202 W 0.776 1.632
203 V 0.517 1.325
218 E 0.988* 1.871
219 P 0.996** 1.879
243 F 0.987* 1.870
264 E 0.848 1.715
265 S 0.712 1.558
266 E 0.609 1.444
269 R 0.909 1.783
317 F 0.638 1.475
338 K 0.905 1.778
351 Q 0.873 1.742
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_Phybrida_S9_FBX1_AB933000)
Pr(w>1) post mean +- SE for w
51 T 0.971* 2.382 +- 0.369
65 S 0.928 2.315 +- 0.481
67 R 0.997** 2.422 +- 0.275
97 C 0.974* 2.386 +- 0.359
117 Y 0.979* 2.395 +- 0.342
118 V 0.958* 2.361 +- 0.407
149 Q 0.976* 2.390 +- 0.352
218 E 0.979* 2.394 +- 0.343
219 P 0.992** 2.414 +- 0.295
243 F 0.980* 2.397 +- 0.338
264 E 0.602 1.774 +- 0.812
269 R 0.766 2.047 +- 0.716
338 K 0.798 2.101 +- 0.685
351 Q 0.715 1.961 +- 0.763
