--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Nov 04 01:34:25 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/S7/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S7/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/S7/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -7782.32 -7800.45
2 -7782.68 -7803.97
--------------------------------------
TOTAL -7782.49 -7803.31
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/revmuscle/S7/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S7/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/S7/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.553233 0.003871 1.437319 1.671137 1.551009 1385.29 1443.15 1.001
r(A<->C){all} 0.115391 0.000133 0.093592 0.137973 0.115214 989.25 1018.81 1.000
r(A<->G){all} 0.302176 0.000330 0.267441 0.336896 0.301816 614.19 752.83 1.000
r(A<->T){all} 0.072014 0.000051 0.058025 0.085796 0.071903 1171.39 1217.05 1.000
r(C<->G){all} 0.157418 0.000226 0.128778 0.187145 0.157070 867.89 868.18 1.001
r(C<->T){all} 0.266934 0.000290 0.231463 0.298372 0.266824 639.01 709.83 1.001
r(G<->T){all} 0.086068 0.000079 0.069042 0.103553 0.085636 1033.08 1096.29 1.000
pi(A){all} 0.299850 0.000118 0.279532 0.321422 0.299853 1003.20 1138.79 1.000
pi(C){all} 0.172852 0.000076 0.156320 0.190205 0.172704 775.36 891.89 1.000
pi(G){all} 0.190047 0.000085 0.171463 0.207282 0.189971 1060.84 1124.68 1.000
pi(T){all} 0.337251 0.000130 0.314160 0.358406 0.337220 997.68 1011.36 1.000
alpha{1,2} 0.865064 0.012832 0.641303 1.075559 0.855112 1044.56 1180.82 1.000
alpha{3} 1.978792 0.208319 1.222132 2.901614 1.909816 1501.00 1501.00 1.000
pinvar{all} 0.030614 0.000634 0.000024 0.080777 0.024200 1365.39 1433.19 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 -5237.548298
Model 2: PositiveSelection -5201.08564
Model 0: one-ratio -5367.579411
Model 3: discrete -5200.812648
Model 7: beta -5248.360468
Model 8: beta&w>1 -5202.288935
Model 0 vs 1 260.062226
Model 2 vs 1 72.92531599999893
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S7_SFBB1)
Pr(w>1) post mean +- SE for w
7 N 0.992** 3.724
13 R 1.000** 3.744
17 P 0.956* 3.625
46 L 0.988* 3.712
53 E 0.964* 3.648
66 A 0.585 2.607
94 R 0.928 3.547
102 I 1.000** 3.745
104 T 0.999** 3.744
150 T 0.569 2.562
165 E 0.750 3.060
168 C 0.983* 3.698
184 T 1.000** 3.745
186 E 0.991** 3.721
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: S7_SFBB1)
Pr(w>1) post mean +- SE for w
7 N 0.991** 3.747 +- 0.540
13 R 0.999** 3.773 +- 0.478
17 P 0.949 3.624 +- 0.760
46 L 0.986* 3.735 +- 0.569
53 E 0.961* 3.666 +- 0.707
66 A 0.568 2.517 +- 1.357
94 R 0.916 3.528 +- 0.883
102 I 1.000** 3.773 +- 0.477
104 T 0.999** 3.772 +- 0.478
150 T 0.554 2.486 +- 1.369
165 E 0.723 2.949 +- 1.259
168 C 0.981* 3.720 +- 0.603
184 T 1.000** 3.774 +- 0.475
186 E 0.990* 3.746 +- 0.546
Model 8 vs 7 92.14306600000054
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S7_SFBB1)
Pr(w>1) post mean +- SE for w
7 N 0.998** 3.112
13 R 1.000** 3.116
17 P 0.989* 3.091
46 L 0.997** 3.108
51 F 0.553 2.098
53 E 0.987* 3.087
55 G 0.706 2.443
66 A 0.863 2.806
94 R 0.981* 3.073
102 I 1.000** 3.116
104 T 1.000** 3.116
121 Q 0.617 2.227
133 Q 0.693 2.411
136 Y 0.567 2.134
150 T 0.826 2.718
151 I 0.619 2.258
165 E 0.941 2.983
168 C 0.995** 3.104
184 T 1.000** 3.116
186 E 0.997** 3.110
214 K 0.743 2.530
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: S7_SFBB1)
Pr(w>1) post mean +- SE for w
7 N 0.997** 3.204 +- 0.567
13 R 1.000** 3.212 +- 0.554
17 P 0.979* 3.158 +- 0.637
46 L 0.994** 3.198 +- 0.578
53 E 0.981* 3.164 +- 0.635
55 G 0.597 2.145 +- 1.145
66 A 0.767 2.586 +- 1.060
94 R 0.965* 3.118 +- 0.690
102 I 1.000** 3.212 +- 0.554
104 T 1.000** 3.212 +- 0.554
121 Q 0.546 2.028 +- 1.187
133 Q 0.595 2.144 +- 1.159
150 T 0.733 2.500 +- 1.102
165 E 0.877 2.878 +- 0.902
168 C 0.992** 3.191 +- 0.589
184 T 1.000** 3.212 +- 0.553
186 E 0.996** 3.202 +- 0.572
214 K 0.627 2.220 +- 1.137
