--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Tue Nov 07 11:33:58 WET 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=CLUSTALW2
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/S2novarevisao/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/S2novarevisao/ClustalW2/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/S2novarevisao/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -8085.47 -8107.94
2 -8085.94 -8105.41
--------------------------------------
TOTAL -8085.68 -8107.32
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/S2novarevisao/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/S2novarevisao/ClustalW2/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/S2novarevisao/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.444742 0.003042 1.338398 1.552694 1.444209 1316.68 1408.84 1.000
r(A<->C){all} 0.103526 0.000113 0.081898 0.123821 0.103355 904.68 1001.19 1.000
r(A<->G){all} 0.296438 0.000310 0.262285 0.329496 0.296411 732.31 823.04 1.000
r(A<->T){all} 0.075199 0.000053 0.061327 0.090161 0.075138 934.70 983.86 1.000
r(C<->G){all} 0.150343 0.000214 0.120390 0.178529 0.150372 842.35 917.42 1.000
r(C<->T){all} 0.287041 0.000298 0.255438 0.323399 0.286469 767.04 792.46 1.000
r(G<->T){all} 0.087453 0.000080 0.069785 0.104779 0.087248 1044.11 1111.76 1.000
pi(A){all} 0.300048 0.000123 0.279477 0.322492 0.299793 860.17 862.38 1.000
pi(C){all} 0.170234 0.000075 0.152097 0.185967 0.170004 909.42 1049.36 1.000
pi(G){all} 0.190285 0.000078 0.173744 0.208339 0.190258 979.38 1049.38 1.000
pi(T){all} 0.339433 0.000136 0.316789 0.362299 0.339284 886.47 913.36 1.001
alpha{1,2} 0.890622 0.015896 0.652998 1.128527 0.872225 1108.53 1163.72 1.000
alpha{3} 1.829502 0.161855 1.087278 2.584057 1.769971 1166.58 1249.10 1.001
pinvar{all} 0.034348 0.000783 0.000046 0.091076 0.027678 1110.38 1158.99 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 -5305.117167
Model 2: PositiveSelection -5276.079396
Model 0: one-ratio -5412.424888
Model 3: discrete -5274.324693
Model 7: beta -5310.74118
Model 8: beta&w>1 -5274.669779
Model 0 vs 1 214.61544199999844
Model 2 vs 1 58.075542000000496
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S2_SFBB1)
Pr(w>1) post mean +- SE for w
10 M 0.800 3.039
27 N 0.985* 3.509
33 R 0.999** 3.547
37 P 0.645 2.644
66 L 0.927 3.364
73 E 0.997** 3.540
85 L 0.745 2.899
86 A 0.541 2.379
113 R 0.887 3.260
121 I 0.999** 3.545
123 T 0.999** 3.547
140 Q 0.687 2.752
169 T 0.788 3.009
187 C 0.544 2.387
203 T 0.998** 3.545
205 E 0.961* 3.449
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: S2_SFBB1)
Pr(w>1) post mean +- SE for w
10 M 0.757 3.011 +- 1.194
27 N 0.980* 3.636 +- 0.577
33 R 0.999** 3.689 +- 0.452
37 P 0.586 2.533 +- 1.322
66 L 0.909 3.438 +- 0.874
73 E 0.996** 3.682 +- 0.473
85 L 0.690 2.818 +- 1.262
113 R 0.855 3.280 +- 1.017
121 I 0.998** 3.688 +- 0.457
123 T 0.999** 3.689 +- 0.452
140 Q 0.644 2.708 +- 1.314
169 T 0.748 2.991 +- 1.210
203 T 0.998** 3.687 +- 0.459
205 E 0.951* 3.556 +- 0.720
Model 8 vs 7 72.1428020000003
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S2_SFBB1)
Pr(w>1) post mean +- SE for w
10 M 0.919 2.789
27 N 0.995** 2.947
33 R 1.000** 2.956
37 P 0.854 2.652
66 L 0.972* 2.899
71 F 0.575 2.066
73 E 0.998** 2.954
75 G 0.679 2.281
85 L 0.902 2.754
86 A 0.791 2.519
113 R 0.959* 2.873
121 I 0.999** 2.956
123 T 1.000** 2.956
140 Q 0.840 2.618
152 Q 0.515 1.921
155 Y 0.588 2.095
159 A 0.512 1.932
169 T 0.906 2.760
184 E 0.643 2.209
187 C 0.781 2.496
203 T 0.999** 2.956
205 E 0.985* 2.927
255 D 0.674 2.275
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: S2_SFBB1)
Pr(w>1) post mean +- SE for w
10 M 0.890 2.739 +- 0.824
27 N 0.993** 2.994 +- 0.564
33 R 1.000** 3.011 +- 0.540
37 P 0.799 2.506 +- 0.938
66 L 0.962* 2.919 +- 0.663
71 F 0.545 1.889 +- 0.990
73 E 0.998** 3.008 +- 0.545
75 G 0.627 2.087 +- 1.019
85 L 0.859 2.658 +- 0.867
86 A 0.731 2.338 +- 0.991
113 R 0.941 2.864 +- 0.716
121 I 0.999** 3.010 +- 0.541
123 T 1.000** 3.011 +- 0.540
140 Q 0.807 2.537 +- 0.953
152 Q 0.507 1.814 +- 1.036
155 Y 0.554 1.910 +- 0.989
169 T 0.878 2.711 +- 0.848
184 E 0.587 1.981 +- 0.995
187 C 0.726 2.327 +- 1.000
203 T 0.999** 3.010 +- 0.541
205 E 0.981* 2.965 +- 0.606
255 D 0.615 2.051 +- 1.004
