--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 03 23:23:50 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/S28_wo1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S28_wo1/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/S28_wo1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -8580.49 -8609.32
2 -8580.02 -8598.48
--------------------------------------
TOTAL -8580.23 -8608.63
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/revmuscle/S28_wo1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S28_wo1/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/S28_wo1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.646481 0.003963 1.528431 1.772811 1.645427 1459.15 1480.08 1.000
r(A<->C){all} 0.118400 0.000122 0.097198 0.139883 0.118011 775.10 781.84 1.000
r(A<->G){all} 0.304722 0.000307 0.268877 0.336311 0.304800 549.24 685.32 1.000
r(A<->T){all} 0.074895 0.000047 0.062330 0.088924 0.074660 1024.83 1123.95 1.004
r(C<->G){all} 0.152320 0.000205 0.124008 0.180206 0.152193 851.82 935.12 1.000
r(C<->T){all} 0.261648 0.000260 0.230231 0.292136 0.261576 644.32 660.60 1.000
r(G<->T){all} 0.088015 0.000072 0.071137 0.103973 0.087939 927.83 964.32 1.000
pi(A){all} 0.294757 0.000115 0.274506 0.316149 0.294674 798.74 865.63 1.000
pi(C){all} 0.170287 0.000072 0.153836 0.186846 0.170138 825.45 829.85 1.001
pi(G){all} 0.192695 0.000077 0.175631 0.209711 0.192589 799.28 868.67 1.000
pi(T){all} 0.342261 0.000126 0.321489 0.365048 0.341969 811.35 944.62 1.001
alpha{1,2} 0.902766 0.013307 0.699101 1.139728 0.889667 1328.82 1414.91 1.000
alpha{3} 2.136957 0.208637 1.350523 3.063191 2.067187 1388.02 1444.51 1.000
pinvar{all} 0.028142 0.000545 0.000020 0.074881 0.022814 1375.26 1438.13 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 -5566.357101
Model 2: PositiveSelection -5534.330081
Model 0: one-ratio -5706.64906
Model 3: discrete -5534.182828
Model 7: beta -5575.884069
Model 8: beta&w>1 -5538.354717
Model 0 vs 1 280.58391800000027
Model 2 vs 1 64.05403999999908
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S28_SFBB1)
Pr(w>1) post mean +- SE for w
5 N 0.933 3.664
11 R 0.999** 3.852
51 E 0.997** 3.844
64 A 0.872 3.489
76 G 0.611 2.744
100 I 0.997** 3.845
102 T 1.000** 3.853
163 E 0.639 2.825
166 C 0.967* 3.759
182 T 1.000** 3.854
184 E 0.904 3.578
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: S28_SFBB1)
Pr(w>1) post mean +- SE for w
5 N 0.889 3.653 +- 1.082
11 R 0.999** 4.027 +- 0.608
51 E 0.996** 4.017 +- 0.631
64 A 0.811 3.405 +- 1.267
76 G 0.529 2.528 +- 1.492
100 I 0.996** 4.018 +- 0.629
102 T 1.000** 4.028 +- 0.605
163 E 0.535 2.506 +- 1.450
166 C 0.957* 3.897 +- 0.849
182 T 1.000** 4.030 +- 0.602
184 E 0.862 3.578 +- 1.165
Model 8 vs 7 75.05870399999912
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S28_SFBB1)
Pr(w>1) post mean +- SE for w
5 N 0.975* 3.284
11 R 1.000** 3.343
44 L 0.695 2.596
51 E 0.998** 3.339
64 A 0.947 3.214
76 G 0.779 2.798
91 S 0.627 2.414
100 I 0.999** 3.340
102 T 1.000** 3.343
163 E 0.848 2.973
166 C 0.985* 3.306
182 T 1.000** 3.344
184 E 0.956* 3.237
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: S28_SFBB1)
Pr(w>1) post mean +- SE for w
5 N 0.958* 3.451 +- 0.626
11 R 1.000** 3.567 +- 0.354
44 L 0.575 2.396 +- 1.312
51 E 0.998** 3.562 +- 0.371
64 A 0.918 3.340 +- 0.798
76 G 0.697 2.733 +- 1.251
91 S 0.534 2.289 +- 1.353
100 I 0.998** 3.563 +- 0.367
102 T 1.000** 3.567 +- 0.352
163 E 0.750 2.870 +- 1.160
166 C 0.980* 3.514 +- 0.511
182 T 1.000** 3.568 +- 0.350
184 E 0.936 3.393 +- 0.730
