--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Nov 04 02:14:22 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/revmuscle/S9/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S9/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/revmuscle/S9/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -8659.11 -8678.27
2 -8660.05 -8685.87
--------------------------------------
TOTAL -8659.47 -8685.18
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/revmuscle/S9/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S9/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/revmuscle/S9/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.558293 0.003613 1.446847 1.677442 1.556226 1416.88 1458.94 1.000
r(A<->C){all} 0.107070 0.000111 0.087674 0.128343 0.106703 832.61 970.19 1.000
r(A<->G){all} 0.296124 0.000334 0.260845 0.332910 0.295945 595.85 769.66 1.000
r(A<->T){all} 0.075597 0.000052 0.061279 0.088632 0.075333 1160.76 1161.35 1.001
r(C<->G){all} 0.168509 0.000213 0.138106 0.195547 0.168272 745.59 938.09 1.000
r(C<->T){all} 0.278580 0.000299 0.245780 0.311627 0.278315 831.29 879.13 1.000
r(G<->T){all} 0.074119 0.000066 0.058141 0.089658 0.073852 973.41 1124.51 1.000
pi(A){all} 0.303728 0.000123 0.283066 0.325835 0.303460 906.22 929.80 1.000
pi(C){all} 0.169499 0.000071 0.153626 0.186668 0.169281 1059.32 1085.98 1.001
pi(G){all} 0.186026 0.000080 0.168376 0.202547 0.185892 766.40 883.99 1.000
pi(T){all} 0.340747 0.000136 0.318077 0.363741 0.340559 892.74 897.73 1.001
alpha{1,2} 0.850847 0.012325 0.651088 1.081700 0.838039 1051.10 1236.90 1.000
alpha{3} 1.624522 0.108844 1.092232 2.319610 1.580005 1306.98 1316.63 1.000
pinvar{all} 0.033997 0.000743 0.000004 0.088343 0.027645 1295.71 1299.51 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 -5488.987427
Model 2: PositiveSelection -5451.403633
Model 0: one-ratio -5622.903996
Model 3: discrete -5449.402515
Model 7: beta -5495.653586
Model 8: beta&w>1 -5451.373108
Model 0 vs 1 267.83313799999996
Model 2 vs 1 75.16758800000025
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S3_S9_AB539854_MdFBX11)
Pr(w>1) post mean +- SE for w
14 T 0.986* 3.484
20 N 1.000** 3.519
24 Q 0.989* 3.491
53 L 0.955* 3.407
58 Y 0.724 2.823
60 L 0.991** 3.498
62 L 0.784 2.975
73 A 0.729 2.836
99 K 0.970* 3.443
107 V 0.999** 3.517
109 R 1.000** 3.518
138 R 0.597 2.505
155 T 0.785 2.977
170 K 0.964* 3.430
173 S 0.784 2.974
189 T 1.000** 3.519
191 A 0.978* 3.464
219 K 0.757 2.908
242 E 0.511 2.287
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: S3_S9_AB539854_MdFBX11)
Pr(w>1) post mean +- SE for w
14 T 0.980* 3.555 +- 0.485
20 N 1.000** 3.608 +- 0.330
24 Q 0.985* 3.569 +- 0.453
53 L 0.940 3.450 +- 0.692
58 Y 0.653 2.677 +- 1.243
60 L 0.989* 3.581 +- 0.422
62 L 0.728 2.885 +- 1.180
73 A 0.661 2.702 +- 1.240
99 K 0.960* 3.502 +- 0.603
107 V 0.999** 3.606 +- 0.337
109 R 0.999** 3.607 +- 0.332
138 R 0.529 2.361 +- 1.303
155 T 0.730 2.891 +- 1.179
170 K 0.951* 3.478 +- 0.643
173 S 0.728 2.884 +- 1.180
189 T 1.000** 3.609 +- 0.327
191 A 0.971* 3.533 +- 0.541
219 K 0.695 2.793 +- 1.213
Model 8 vs 7 88.56095600000117
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S3_S9_AB539854_MdFBX11)
Pr(w>1) post mean +- SE for w
14 T 0.994** 2.991
20 N 1.000** 3.003
24 Q 0.995** 2.992
53 L 0.979* 2.960
58 Y 0.876 2.742
60 L 0.995** 2.993
62 L 0.893 2.777
72 T 0.533 2.003
73 A 0.872 2.731
85 R 0.589 2.113
99 K 0.986* 2.973
107 V 1.000** 3.002
109 R 1.000** 3.003
126 Q 0.658 2.267
138 R 0.762 2.493
141 Y 0.635 2.229
155 T 0.890 2.769
170 K 0.985* 2.972
173 S 0.898 2.787
189 T 1.000** 3.003
191 A 0.990* 2.981
214 R 0.621 2.193
219 K 0.881 2.751
239 R 0.639 2.228
242 E 0.734 2.438
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: S3_S9_AB539854_MdFBX11)
Pr(w>1) post mean +- SE for w
14 T 0.993** 2.771 +- 0.481
20 N 1.000** 2.786 +- 0.460
24 Q 0.994** 2.773 +- 0.480
53 L 0.977* 2.736 +- 0.530
58 Y 0.874 2.492 +- 0.722
60 L 0.995** 2.775 +- 0.478
62 L 0.893 2.544 +- 0.708
72 T 0.629 1.966 +- 0.893
73 A 0.871 2.491 +- 0.735
85 R 0.651 2.022 +- 0.923
99 K 0.985* 2.752 +- 0.509
107 V 0.999** 2.785 +- 0.462
109 R 1.000** 2.785 +- 0.461
126 Q 0.705 2.132 +- 0.893
138 R 0.784 2.304 +- 0.843
141 Y 0.704 2.119 +- 0.855
155 T 0.890 2.539 +- 0.717
170 K 0.983* 2.748 +- 0.512
173 S 0.897 2.553 +- 0.700
189 T 1.000** 2.786 +- 0.460
191 A 0.989* 2.762 +- 0.496
214 R 0.686 2.082 +- 0.875
219 K 0.880 2.512 +- 0.724
239 R 0.693 2.105 +- 0.892
242 E 0.764 2.248 +- 0.833
