--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Tue Nov 07 11:34:11 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/S2novarevisao/Muscle/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/S2novarevisao/Muscle/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/Muscle/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -7958.92 -7975.10
2 -7958.46 -7975.31
--------------------------------------
TOTAL -7958.66 -7975.21
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/S2novarevisao/Muscle/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/S2novarevisao/Muscle/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/Muscle/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.408772 0.003127 1.299026 1.515676 1.407621 1501.00 1501.00 1.000
r(A<->C){all} 0.100019 0.000115 0.079134 0.120578 0.099491 1084.52 1093.45 1.001
r(A<->G){all} 0.297995 0.000327 0.263438 0.332558 0.297953 725.85 856.74 1.000
r(A<->T){all} 0.072872 0.000050 0.059291 0.086684 0.072712 977.18 1036.35 1.000
r(C<->G){all} 0.156261 0.000217 0.128730 0.185490 0.156025 773.98 881.89 1.000
r(C<->T){all} 0.288952 0.000317 0.255188 0.323698 0.288482 850.16 879.01 1.000
r(G<->T){all} 0.083901 0.000079 0.066795 0.101750 0.083641 930.48 933.69 1.000
pi(A){all} 0.300246 0.000116 0.280133 0.322124 0.300162 870.76 979.08 1.001
pi(C){all} 0.169117 0.000070 0.152474 0.184963 0.169014 838.18 912.91 1.000
pi(G){all} 0.190385 0.000079 0.172544 0.207438 0.190125 1018.29 1114.43 1.000
pi(T){all} 0.340253 0.000136 0.315430 0.361002 0.340425 575.67 758.53 1.000
alpha{1,2} 0.806107 0.012028 0.626842 1.043898 0.792194 925.20 1213.10 1.000
alpha{3} 1.787298 0.149750 1.119227 2.559372 1.735916 1204.48 1204.93 1.000
pinvar{all} 0.032112 0.000742 0.000005 0.085947 0.024958 1248.43 1311.74 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 -5420.915317
Model 2: PositiveSelection -5390.19306
Model 0: one-ratio -5530.65893
Model 3: discrete -5387.642397
Model 7: beta -5426.083543
Model 8: beta&w>1 -5388.163064
Model 0 vs 1 219.48722599999928
Model 2 vs 1 61.44451400000071
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 0.826 3.086
27 N 0.986* 3.489
33 R 0.999** 3.524
37 P 0.670 2.692
66 L 0.935 3.360
73 E 0.997** 3.518
85 L 0.756 2.910
86 A 0.563 2.422
113 S 0.634 2.601
114 R 0.929 3.346
122 I 0.999** 3.522
124 T 0.999** 3.523
141 Q 0.715 2.805
153 Q 0.529 2.336
170 T 0.809 3.044
188 C 0.561 2.418
204 T 0.999** 3.522
206 E 0.975* 3.462
257 T 0.648 2.636
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 0.784 3.068 +- 1.137
27 N 0.982* 3.611 +- 0.538
33 R 0.999** 3.659 +- 0.413
37 P 0.605 2.578 +- 1.303
66 L 0.917 3.434 +- 0.826
73 E 0.997** 3.653 +- 0.434
85 L 0.697 2.825 +- 1.240
113 S 0.575 2.505 +- 1.323
114 R 0.908 3.407 +- 0.854
122 I 0.999** 3.658 +- 0.419
124 T 0.999** 3.659 +- 0.414
141 Q 0.666 2.754 +- 1.282
170 T 0.768 3.028 +- 1.165
204 T 0.999** 3.657 +- 0.419
206 E 0.969* 3.576 +- 0.612
257 T 0.574 2.485 +- 1.304
Model 8 vs 7 75.84095799999886
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 0.927 2.798
27 N 0.995** 2.939
33 R 1.000** 2.948
37 P 0.859 2.655
66 L 0.974* 2.894
71 F 0.585 2.082
73 E 0.999** 2.946
75 G 0.698 2.316
85 L 0.902 2.746
86 A 0.795 2.520
113 S 0.807 2.542
114 R 0.973* 2.892
122 I 0.999** 2.948
124 T 1.000** 2.948
141 Q 0.852 2.638
153 Q 0.738 2.396
156 Y 0.607 2.130
160 A 0.510 1.923
170 T 0.912 2.766
185 E 0.669 2.258
188 C 0.785 2.498
204 T 0.999** 2.948
206 E 0.990* 2.928
257 T 0.858 2.653
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 0.919 2.645 +- 0.698
27 N 0.994** 2.823 +- 0.512
33 R 1.000** 2.836 +- 0.494
37 P 0.845 2.466 +- 0.798
66 L 0.970* 2.767 +- 0.583
71 F 0.637 1.993 +- 0.902
73 E 0.998** 2.834 +- 0.498
75 G 0.713 2.163 +- 0.899
85 L 0.887 2.566 +- 0.743
86 A 0.787 2.331 +- 0.854
98 G 0.554 1.822 +- 0.959
113 S 0.805 2.380 +- 0.858
114 R 0.968* 2.762 +- 0.587
122 I 0.999** 2.835 +- 0.495
124 T 1.000** 2.836 +- 0.494
141 Q 0.849 2.487 +- 0.816
153 Q 0.747 2.248 +- 0.900
156 Y 0.653 2.025 +- 0.895
160 A 0.589 1.885 +- 0.898
170 T 0.906 2.616 +- 0.725
185 E 0.688 2.098 +- 0.886
188 C 0.780 2.316 +- 0.864
204 T 0.999** 2.835 +- 0.495
206 E 0.989* 2.811 +- 0.530
257 T 0.837 2.443 +- 0.800
