--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 03 19:38:05 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/S10/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S10/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/S10/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -8080.82 -8098.90
2 -8080.55 -8098.70
--------------------------------------
TOTAL -8080.68 -8098.81
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/revmuscle/S10/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S10/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/S10/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.471030 0.003284 1.365205 1.592360 1.469561 1257.88 1379.44 1.001
r(A<->C){all} 0.115330 0.000127 0.094336 0.137782 0.115189 948.28 1034.06 1.000
r(A<->G){all} 0.305625 0.000304 0.273833 0.340291 0.305149 725.27 770.12 1.000
r(A<->T){all} 0.072161 0.000049 0.059511 0.086575 0.071908 1072.54 1079.48 1.000
r(C<->G){all} 0.153613 0.000220 0.122973 0.180978 0.153229 979.98 1022.01 1.002
r(C<->T){all} 0.268540 0.000274 0.238470 0.302220 0.268326 692.23 776.93 1.001
r(G<->T){all} 0.084731 0.000077 0.068001 0.101918 0.084730 970.27 982.82 1.000
pi(A){all} 0.297933 0.000117 0.278158 0.319947 0.298072 818.86 894.36 1.000
pi(C){all} 0.170297 0.000068 0.154141 0.186600 0.170191 976.67 1035.62 1.000
pi(G){all} 0.187566 0.000075 0.170474 0.204133 0.187396 965.48 978.88 1.000
pi(T){all} 0.344204 0.000128 0.322955 0.366896 0.344177 877.40 907.52 1.000
alpha{1,2} 0.924174 0.017807 0.688301 1.195225 0.906571 1181.70 1237.15 1.000
alpha{3} 1.711391 0.146508 1.064725 2.488710 1.650764 1061.09 1281.04 1.000
pinvar{all} 0.036911 0.000857 0.000043 0.096179 0.030339 1256.00 1378.50 1.001
------------------------------------------------------------------------------------------------------
* 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 -4803.007531
Model 2: PositiveSelection -4769.267141
Model 0: one-ratio -4927.143177
Model 3: discrete -4768.761995
Model 7: beta -4813.700505
Model 8: beta&w>1 -4770.729276
Model 0 vs 1 248.27129199999945
Model 2 vs 1 67.48077999999987
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S10_SFBB1)
Pr(w>1) post mean +- SE for w
10 N 0.973* 3.435
16 R 0.999** 3.499
20 P 0.999** 3.500
49 L 0.997** 3.495
54 F 0.830 3.078
56 E 0.972* 3.431
81 G 0.533 2.333
93 Q 0.520 2.300
97 R 0.890 3.226
105 I 0.991** 3.481
107 T 0.999** 3.499
124 Q 0.630 2.576
153 T 0.906 3.266
168 E 0.800 3.001
171 C 0.986* 3.468
187 T 1.000** 3.502
189 E 0.948 3.371
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: S10_SFBB1)
Pr(w>1) post mean +- SE for w
10 N 0.959* 3.521 +- 0.650
16 R 0.999** 3.633 +- 0.415
20 P 0.999** 3.634 +- 0.413
49 L 0.996** 3.628 +- 0.431
54 F 0.765 2.983 +- 1.144
56 E 0.964* 3.543 +- 0.629
97 R 0.847 3.215 +- 1.004
105 I 0.989* 3.609 +- 0.484
107 T 0.998** 3.633 +- 0.417
124 Q 0.567 2.473 +- 1.318
153 T 0.875 3.296 +- 0.943
168 E 0.726 2.875 +- 1.190
171 C 0.982* 3.590 +- 0.529
187 T 1.000** 3.637 +- 0.403
189 E 0.931 3.450 +- 0.771
Model 8 vs 7 85.94245799999953
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S10_SFBB1)
Pr(w>1) post mean +- SE for w
10 N 0.994** 2.956
16 R 1.000** 2.968
20 P 1.000** 2.968
49 L 0.999** 2.967
54 F 0.954* 2.873
56 E 0.989* 2.946
58 G 0.613 2.137
68 L 0.558 2.024
69 A 0.780 2.501
81 G 0.780 2.499
93 Q 0.739 2.406
95 R 0.736 2.409
96 S 0.636 2.181
97 R 0.967* 2.899
105 I 0.997** 2.962
107 T 1.000** 2.968
124 Q 0.806 2.550
137 Y 0.555 2.007
139 Y 0.601 2.124
153 T 0.967* 2.900
168 E 0.945 2.855
171 C 0.995** 2.959
187 T 1.000** 2.969
189 E 0.982* 2.931
217 K 0.707 2.344
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: S10_SFBB1)
Pr(w>1) post mean +- SE for w
10 N 0.995** 2.638 +- 0.385
16 R 1.000** 2.648 +- 0.368
20 P 1.000** 2.648 +- 0.368
49 L 0.999** 2.647 +- 0.370
54 F 0.963* 2.570 +- 0.476
56 E 0.990** 2.630 +- 0.404
58 G 0.732 2.110 +- 0.827
68 L 0.712 2.066 +- 0.824
69 A 0.846 2.332 +- 0.700
81 G 0.841 2.326 +- 0.716
93 Q 0.807 2.260 +- 0.770
95 R 0.826 2.285 +- 0.710
96 S 0.738 2.122 +- 0.835
97 R 0.972* 2.592 +- 0.456
105 I 0.997** 2.643 +- 0.379
107 T 0.999** 2.648 +- 0.368
124 Q 0.850 2.349 +- 0.721
136 Q 0.503 1.670 +- 0.917
137 Y 0.691 2.027 +- 0.858
139 Y 0.749 2.139 +- 0.785
153 T 0.972* 2.594 +- 0.459
168 E 0.957* 2.556 +- 0.491
171 C 0.996** 2.641 +- 0.384
187 T 1.000** 2.649 +- 0.366
189 E 0.984* 2.618 +- 0.422
217 K 0.803 2.243 +- 0.748
