--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Tue Oct 31 18:21:44 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/S1_18Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S1_18Malus/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/S1_18Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -8479.63 -8499.87
2 -8479.36 -8500.26
--------------------------------------
TOTAL -8479.49 -8500.09
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Srevisao/S1_18Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S1_18Malus/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/S1_18Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.641477 0.003773 1.523864 1.763089 1.641311 1382.34 1420.51 1.000
r(A<->C){all} 0.116718 0.000121 0.095979 0.139254 0.116461 981.89 1004.16 1.000
r(A<->G){all} 0.297573 0.000314 0.263542 0.331833 0.297515 785.28 887.87 1.001
r(A<->T){all} 0.072904 0.000055 0.058607 0.086703 0.072651 610.02 882.05 1.000
r(C<->G){all} 0.150503 0.000200 0.123780 0.178502 0.149947 881.76 1014.54 1.000
r(C<->T){all} 0.269613 0.000289 0.239373 0.305731 0.268894 782.75 783.82 1.000
r(G<->T){all} 0.092690 0.000078 0.075987 0.110160 0.092362 1005.27 1154.30 1.000
pi(A){all} 0.296435 0.000116 0.274981 0.317367 0.296339 775.83 909.17 1.000
pi(C){all} 0.170889 0.000073 0.153653 0.186329 0.170796 833.37 941.37 1.000
pi(G){all} 0.189965 0.000079 0.171588 0.206267 0.189872 873.65 985.30 1.000
pi(T){all} 0.342710 0.000129 0.320284 0.364795 0.342453 1100.35 1136.58 1.000
alpha{1,2} 0.844618 0.010717 0.670832 1.059716 0.833556 1244.18 1295.08 1.000
alpha{3} 1.934298 0.163856 1.236261 2.732345 1.886747 1258.27 1339.81 1.000
pinvar{all} 0.026634 0.000518 0.000008 0.072645 0.020524 1257.74 1292.78 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 -6252.628628
Model 2: PositiveSelection -6216.667031
Model 0: one-ratio -6385.849692
Model 3: discrete -6215.149793
Model 7: beta -6260.066885
Model 8: beta&w>1 -6214.282808
Model 0 vs 1 266.4421279999988
Model 2 vs 1 71.92319400000088
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S1_SFBB1)
Pr(w>1) post mean +- SE for w
40 N 1.000** 3.403
46 R 1.000** 3.403
50 P 0.996** 3.395
79 L 0.999** 3.401
84 F 0.861 3.069
86 E 0.986* 3.370
88 G 0.760 2.826
98 L 0.527 2.266
99 A 0.891 3.142
125 R 0.514 2.235
132 I 0.966* 3.322
134 T 0.999** 3.400
151 Q 0.884 3.125
162 E 0.536 2.289
195 E 0.601 2.445
214 T 0.996** 3.395
216 E 0.944 3.268
244 K 0.939 3.257
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: S1_SFBB1)
Pr(w>1) post mean +- SE for w
40 N 1.000** 3.531 +- 0.260
46 R 1.000** 3.531 +- 0.262
50 P 0.996** 3.522 +- 0.300
79 L 0.999** 3.529 +- 0.268
84 F 0.839 3.113 +- 0.954
86 E 0.986* 3.495 +- 0.395
88 G 0.728 2.830 +- 1.137
99 A 0.876 3.210 +- 0.865
132 I 0.963* 3.438 +- 0.538
134 T 0.999** 3.528 +- 0.276
151 Q 0.876 3.216 +- 0.866
195 E 0.555 2.386 +- 1.252
214 T 0.996** 3.522 +- 0.300
216 E 0.938 3.371 +- 0.660
244 K 0.930 3.351 +- 0.688
Model 8 vs 7 91.5681540000005
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S1_SFBB1)
Pr(w>1) post mean +- SE for w
2 R 0.593 2.063
23 M 0.530 1.936
40 N 1.000** 2.918
46 R 1.000** 2.918
50 P 0.999** 2.916
79 L 1.000** 2.918
84 F 0.956* 2.829
86 E 0.994** 2.906
88 G 0.912 2.738
98 L 0.783 2.472
99 A 0.963* 2.844
110 G 0.590 2.055
125 R 0.766 2.436
132 I 0.988* 2.893
134 T 0.999** 2.917
151 Q 0.949 2.813
162 E 0.792 2.491
163 Q 0.526 1.918
166 Y 0.607 2.112
180 T 0.532 1.935
195 E 0.842 2.595
198 C 0.639 2.169
214 T 0.998** 2.915
216 E 0.980* 2.877
244 K 0.980* 2.878
267 T 0.691 2.282
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: S1_SFBB1)
Pr(w>1) post mean +- SE for w
2 R 0.626 1.980 +- 0.953
23 M 0.584 1.883 +- 0.934
40 N 1.000** 2.841 +- 0.482
46 R 1.000** 2.840 +- 0.482
50 P 0.999** 2.838 +- 0.486
79 L 1.000** 2.840 +- 0.483
84 F 0.943 2.704 +- 0.637
86 E 0.994** 2.827 +- 0.504
88 G 0.894 2.587 +- 0.731
98 L 0.769 2.291 +- 0.864
99 A 0.956* 2.736 +- 0.611
110 G 0.623 1.968 +- 0.950
125 R 0.756 2.262 +- 0.875
132 I 0.987* 2.810 +- 0.527
134 T 0.999** 2.840 +- 0.484
151 Q 0.946 2.719 +- 0.639
162 E 0.776 2.305 +- 0.859
163 Q 0.576 1.876 +- 0.966
166 Y 0.643 2.002 +- 0.888
180 T 0.582 1.881 +- 0.947
195 E 0.816 2.397 +- 0.821
198 C 0.662 2.051 +- 0.915
214 T 0.998** 2.837 +- 0.487
216 E 0.977* 2.787 +- 0.556
244 K 0.976* 2.784 +- 0.558
267 T 0.694 2.113 +- 0.889
