--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 03 11:19:58 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/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S5_16Malus/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/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -7545.50 -7563.99
2 -7544.86 -7568.18
--------------------------------------
TOTAL -7545.13 -7567.51
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Srevisao1/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S5_16Malus/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/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.469208 0.003508 1.350087 1.578394 1.468084 1498.65 1499.82 1.000
r(A<->C){all} 0.107501 0.000134 0.084432 0.129230 0.106798 1008.14 1015.87 1.000
r(A<->G){all} 0.320348 0.000335 0.284494 0.356604 0.319870 903.62 940.71 1.001
r(A<->T){all} 0.083122 0.000065 0.068407 0.099767 0.082883 1081.42 1179.92 1.000
r(C<->G){all} 0.143599 0.000213 0.115425 0.172392 0.143039 1013.84 1015.05 1.000
r(C<->T){all} 0.262472 0.000285 0.228995 0.294284 0.262325 772.45 914.42 1.000
r(G<->T){all} 0.082959 0.000082 0.066133 0.102474 0.082508 960.09 971.38 1.000
pi(A){all} 0.292989 0.000114 0.272272 0.313511 0.292875 947.09 982.35 1.001
pi(C){all} 0.174676 0.000076 0.158774 0.192560 0.174447 1044.93 1074.65 1.000
pi(G){all} 0.193692 0.000082 0.175236 0.210526 0.193632 785.24 825.35 1.000
pi(T){all} 0.338643 0.000135 0.315395 0.360700 0.338227 840.18 941.82 1.002
alpha{1,2} 1.007668 0.037610 0.685566 1.371147 0.978509 1063.82 1103.30 1.000
alpha{3} 1.525199 0.159300 0.912001 2.316682 1.448358 1127.18 1285.60 1.000
pinvar{all} 0.060690 0.001948 0.000012 0.146064 0.051403 1026.57 1096.92 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 -3660.050783
Model 2: PositiveSelection -3636.130604
Model 0: one-ratio -3740.088089
Model 3: discrete -3633.973648
Model 7: beta -3659.557345
Model 8: beta&w>1 -3633.174241
Model 0 vs 1 160.07461199999943
Model 2 vs 1 47.84035800000038
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S5_SFBB1)
Pr(w>1) post mean +- SE for w
8 L 0.560 2.662
35 R 0.872 3.590
43 I 0.999** 3.967
45 T 0.999** 3.968
62 Q 0.830 3.464
74 Q 0.542 2.611
77 Y 0.677 3.011
106 E 0.997** 3.962
109 C 0.952* 3.827
125 T 1.000** 3.970
127 E 0.964* 3.864
155 K 0.683 3.028
175 P 0.734 3.180
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: S5_SFBB1)
Pr(w>1) post mean +- SE for w
35 R 0.823 3.567 +- 1.326
43 I 0.999** 4.175 +- 0.691
45 T 0.999** 4.177 +- 0.687
62 Q 0.793 3.497 +- 1.404
77 Y 0.602 2.824 +- 1.558
106 E 0.996** 4.167 +- 0.707
109 C 0.936 3.966 +- 1.010
125 T 1.000** 4.179 +- 0.683
127 E 0.953* 4.023 +- 0.940
155 K 0.606 2.841 +- 1.559
175 P 0.674 3.084 +- 1.541
Model 8 vs 7 52.766208000000006
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S5_SFBB1)
Pr(w>1) post mean +- SE for w
8 L 0.706 2.673
20 G 0.589 2.374
35 R 0.917 3.197
43 I 0.999** 3.401
45 T 0.999** 3.402
62 Q 0.878 3.097
74 Q 0.666 2.566
77 Y 0.794 2.892
106 E 0.997** 3.396
109 C 0.968* 3.324
125 T 1.000** 3.403
127 E 0.975* 3.342
155 K 0.792 2.886
175 P 0.829 2.976
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: S5_SFBB1)
Pr(w>1) post mean +- SE for w
8 L 0.621 2.390 +- 1.262
20 G 0.519 2.114 +- 1.268
35 R 0.879 3.145 +- 1.036
43 I 0.999** 3.499 +- 0.680
45 T 0.999** 3.500 +- 0.678
62 Q 0.845 3.064 +- 1.120
74 Q 0.600 2.354 +- 1.303
77 Y 0.721 2.680 +- 1.229
106 E 0.997** 3.492 +- 0.690
109 C 0.958* 3.381 +- 0.840
125 T 1.000** 3.501 +- 0.676
127 E 0.968* 3.411 +- 0.806
155 K 0.719 2.677 +- 1.239
175 P 0.775 2.851 +- 1.206
