--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 03 12:50:25 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/Srevisao1/S9_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S9_17Malus/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/Srevisao1/S9_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -8704.88 -8725.21
2 -8705.71 -8724.37
--------------------------------------
TOTAL -8705.21 -8724.87
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Srevisao1/S9_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S9_17Malus/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/Srevisao1/S9_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.556977 0.003577 1.442091 1.668117 1.554608 1315.22 1355.80 1.000
r(A<->C){all} 0.104948 0.000105 0.084777 0.124263 0.104751 942.75 948.58 1.000
r(A<->G){all} 0.294567 0.000298 0.260623 0.327120 0.294445 832.30 879.02 1.001
r(A<->T){all} 0.078047 0.000048 0.064481 0.091334 0.077976 979.07 999.68 1.001
r(C<->G){all} 0.172524 0.000224 0.144664 0.203181 0.171876 965.53 979.77 1.000
r(C<->T){all} 0.275964 0.000277 0.245920 0.310454 0.275420 879.66 947.01 1.001
r(G<->T){all} 0.073951 0.000060 0.057922 0.087927 0.073627 989.36 1067.50 1.000
pi(A){all} 0.306393 0.000123 0.283550 0.326761 0.306268 957.80 1043.87 1.001
pi(C){all} 0.167841 0.000069 0.151204 0.183193 0.167887 799.80 932.23 1.000
pi(G){all} 0.185163 0.000085 0.168269 0.203665 0.185053 651.59 916.80 1.000
pi(T){all} 0.340603 0.000129 0.318609 0.362949 0.340455 976.93 1029.16 1.002
alpha{1,2} 0.881009 0.012791 0.667440 1.099467 0.866690 1147.25 1251.24 1.000
alpha{3} 1.646826 0.123508 1.051852 2.351428 1.596708 1293.01 1323.39 1.000
pinvar{all} 0.032508 0.000698 0.000006 0.084746 0.026109 1125.63 1139.03 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 -5433.53787
Model 2: PositiveSelection -5400.745793
Model 0: one-ratio -5562.332691
Model 3: discrete -5399.793851
Model 7: beta -5440.093391
Model 8: beta&w>1 -5401.715001
Model 0 vs 1 257.589641999999
Model 2 vs 1 65.58415400000013
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S3_S9_AB539854_MdFBX11)
Pr(w>1) post mean +- SE for w
14 T 0.837 3.163
20 N 0.999** 3.583
24 Q 0.992** 3.563
53 L 0.934 3.412
58 Y 0.570 2.473
60 L 0.970* 3.507
62 L 0.725 2.874
73 A 0.708 2.828
85 R 0.515 2.330
107 V 0.999** 3.581
109 R 1.000** 3.583
138 R 0.703 2.816
155 T 0.743 2.921
173 S 0.875 3.260
189 T 1.000** 3.584
191 A 0.969* 3.503
219 K 0.681 2.761
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: S3_S9_AB539854_MdFBX11)
Pr(w>1) post mean +- SE for w
14 T 0.780 3.065 +- 1.144
20 N 0.999** 3.696 +- 0.431
24 Q 0.990* 3.670 +- 0.503
53 L 0.914 3.454 +- 0.853
58 Y 0.501 2.303 +- 1.320
60 L 0.964* 3.601 +- 0.653
62 L 0.667 2.766 +- 1.285
73 A 0.645 2.701 +- 1.296
107 V 0.999** 3.694 +- 0.438
109 R 1.000** 3.697 +- 0.429
138 R 0.647 2.718 +- 1.305
155 T 0.690 2.835 +- 1.270
173 S 0.844 3.263 +- 1.044
189 T 1.000** 3.698 +- 0.427
191 A 0.960* 3.587 +- 0.671
219 K 0.618 2.628 +- 1.312
Model 8 vs 7 76.75678000000153
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S3_S9_AB539854_MdFBX11)
Pr(w>1) post mean +- SE for w
14 T 0.935 2.920
20 N 1.000** 3.058
24 Q 0.996** 3.050
53 L 0.969* 2.993
58 Y 0.796 2.619
60 L 0.983* 3.023
62 L 0.863 2.761
72 T 0.506 1.978
73 A 0.860 2.755
85 R 0.702 2.405
107 V 0.999** 3.057
109 R 1.000** 3.058
126 Q 0.562 2.093
138 R 0.843 2.716
155 T 0.866 2.766
170 K 0.734 2.482
173 S 0.938 2.925
189 T 1.000** 3.059
191 A 0.985* 3.027
219 K 0.839 2.709
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: S3_S9_AB539854_MdFBX11)
Pr(w>1) post mean +- SE for w
14 T 0.870 2.884 +- 0.893
20 N 1.000** 3.220 +- 0.500
24 Q 0.994** 3.205 +- 0.529
53 L 0.949 3.091 +- 0.703
58 Y 0.662 2.349 +- 1.113
60 L 0.978* 3.166 +- 0.601
62 L 0.779 2.653 +- 1.040
73 A 0.769 2.627 +- 1.049
85 R 0.593 2.181 +- 1.156
107 V 0.999** 3.219 +- 0.502
109 R 1.000** 3.220 +- 0.499
138 R 0.761 2.610 +- 1.064
155 T 0.793 2.693 +- 1.028
170 K 0.601 2.196 +- 1.133
173 S 0.902 2.972 +- 0.834
189 T 1.000** 3.221 +- 0.498
191 A 0.977* 3.163 +- 0.602
219 K 0.740 2.552 +- 1.077
