--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Tue Oct 31 19:06:37 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/Srevisao/S24_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S24_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/Srevisao/S24_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -7321.50 -7347.97
2 -7321.58 -7340.17
--------------------------------------
TOTAL -7321.54 -7347.27
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Srevisao/S24_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S24_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/Srevisao/S24_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} 1.539856 0.004179 1.413577 1.663098 1.538003 1419.39 1460.20 1.000
r(A<->C){all} 0.119535 0.000141 0.097054 0.143637 0.119242 1036.91 1047.19 1.001
r(A<->G){all} 0.302546 0.000355 0.266413 0.340469 0.302185 770.41 852.92 1.000
r(A<->T){all} 0.075273 0.000059 0.061165 0.091108 0.075001 1197.11 1231.75 1.000
r(C<->G){all} 0.155096 0.000238 0.126628 0.185870 0.154708 1011.64 1044.12 1.000
r(C<->T){all} 0.262896 0.000306 0.227563 0.296297 0.262884 813.12 848.51 1.001
r(G<->T){all} 0.084654 0.000086 0.067474 0.102968 0.084501 934.48 1038.18 1.000
pi(A){all} 0.292303 0.000120 0.272481 0.314436 0.292226 971.69 1114.86 1.000
pi(C){all} 0.175291 0.000076 0.159866 0.194298 0.175144 929.34 1002.94 1.000
pi(G){all} 0.196941 0.000092 0.178868 0.214956 0.196643 805.02 926.84 1.000
pi(T){all} 0.335465 0.000130 0.314464 0.358724 0.335305 1106.01 1117.18 1.000
alpha{1,2} 0.731149 0.010507 0.548909 0.935565 0.717856 1218.11 1271.50 1.000
alpha{3} 2.301397 0.358154 1.293062 3.384344 2.209746 1371.55 1419.94 1.000
pinvar{all} 0.043361 0.001042 0.000004 0.103679 0.036569 1229.64 1296.22 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 -3432.591325
Model 2: PositiveSelection -3412.089337
Model 0: one-ratio -3512.847386
Model 3: discrete -3412.070558
Model 7: beta -3436.013498
Model 8: beta&w>1 -3412.652165
Model 0 vs 1 160.5121220000001
Model 2 vs 1 41.003975999999966
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S24_SFBB1)
Pr(w>1) post mean +- SE for w
2 E 0.911 3.792
43 R 0.631 2.932
50 I 0.999** 4.060
52 T 0.999** 4.061
69 Q 0.609 2.864
84 Y 0.505 2.548
113 E 0.967* 3.963
116 C 0.961* 3.943
132 T 1.000** 4.062
134 E 0.891 3.728
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: S24_SFBB1)
Pr(w>1) post mean +- SE for w
2 E 0.892 3.922 +- 1.238
43 R 0.548 2.687 +- 1.606
50 I 0.999** 4.280 +- 0.764
52 T 0.999** 4.282 +- 0.761
69 Q 0.557 2.774 +- 1.667
113 E 0.946 4.083 +- 1.025
116 C 0.949 4.112 +- 1.025
132 T 1.000** 4.283 +- 0.760
134 E 0.848 3.739 +- 1.337
Model 8 vs 7 46.72266599999966
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S24_SFBB1)
Pr(w>1) post mean +- SE for w
2 E 0.943 3.406
43 R 0.791 3.006
50 I 0.999** 3.554
52 T 1.000** 3.555
69 Q 0.729 2.837
81 Q 0.509 2.246
84 Y 0.710 2.794
113 E 0.984* 3.513
116 C 0.976* 3.493
132 T 1.000** 3.555
134 E 0.940 3.398
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: S24_SFBB1)
Pr(w>1) post mean +- SE for w
2 E 0.929 3.536 +- 1.022
43 R 0.699 2.789 +- 1.364
50 I 0.999** 3.746 +- 0.743
52 T 1.000** 3.746 +- 0.742
69 Q 0.668 2.735 +- 1.434
84 Y 0.607 2.503 +- 1.387
113 E 0.974* 3.663 +- 0.852
116 C 0.969* 3.655 +- 0.878
132 T 1.000** 3.746 +- 0.741
134 E 0.913 3.474 +- 1.057
