--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 03 12:07:39 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/S7_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S7_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/S7_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -7915.22 -7935.70
2 -7915.01 -7933.70
--------------------------------------
TOTAL -7915.11 -7935.13
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Srevisao1/S7_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S7_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/S7_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} 1.589672 0.004085 1.456892 1.705429 1.587433 1043.54 1272.27 1.000
r(A<->C){all} 0.117515 0.000130 0.096695 0.141061 0.117128 988.54 1065.17 1.000
r(A<->G){all} 0.303197 0.000325 0.269052 0.338053 0.302873 817.32 896.92 1.001
r(A<->T){all} 0.074985 0.000054 0.060870 0.089325 0.074626 812.45 1005.82 1.000
r(C<->G){all} 0.154773 0.000220 0.126708 0.184607 0.154099 639.35 895.64 1.000
r(C<->T){all} 0.261598 0.000287 0.226693 0.292429 0.260863 807.44 934.66 1.001
r(G<->T){all} 0.087932 0.000083 0.070630 0.105576 0.087740 1040.30 1081.95 1.000
pi(A){all} 0.300437 0.000122 0.280056 0.322574 0.300170 1009.77 1072.74 1.000
pi(C){all} 0.171786 0.000076 0.155331 0.188508 0.171553 823.94 959.45 1.000
pi(G){all} 0.190639 0.000084 0.172114 0.207917 0.190579 1008.26 1052.83 1.000
pi(T){all} 0.337137 0.000135 0.315026 0.360121 0.337238 938.56 1017.40 1.000
alpha{1,2} 0.839014 0.011414 0.645197 1.044926 0.828820 1369.33 1384.42 1.000
alpha{3} 1.893832 0.173251 1.191888 2.820625 1.837140 1252.48 1376.74 1.000
pinvar{all} 0.031848 0.000651 0.000000 0.081065 0.025492 1414.25 1436.11 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 -5328.244827
Model 2: PositiveSelection -5288.218606
Model 0: one-ratio -5473.429714
Model 3: discrete -5287.815107
Model 7: beta -5340.138853
Model 8: beta&w>1 -5289.777434
Model 0 vs 1 290.36977399999887
Model 2 vs 1 80.05244200000016
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S7_SFBB1)
Pr(w>1) post mean +- SE for w
7 N 0.997** 3.596
13 R 0.999** 3.603
17 P 0.995** 3.591
46 L 0.988* 3.573
53 E 0.934 3.433
66 A 0.650 2.692
93 S 0.999** 3.601
94 R 0.925 3.409
100 I 0.999** 3.602
102 T 0.999** 3.603
131 Q 0.525 2.367
148 T 0.600 2.564
163 E 0.794 3.069
166 C 0.965* 3.513
182 T 1.000** 3.604
184 E 0.992** 3.583
232 P 0.662 2.724
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: S7_SFBB1)
Pr(w>1) post mean +- SE for w
7 N 0.996** 3.657 +- 0.432
13 R 0.999** 3.668 +- 0.402
17 P 0.994** 3.653 +- 0.447
46 L 0.985* 3.629 +- 0.508
53 E 0.922 3.458 +- 0.810
66 A 0.598 2.554 +- 1.300
93 S 0.999** 3.666 +- 0.409
94 R 0.904 3.402 +- 0.862
100 I 0.999** 3.666 +- 0.407
102 T 0.999** 3.667 +- 0.403
148 T 0.552 2.436 +- 1.318
163 E 0.745 2.948 +- 1.179
166 C 0.957* 3.552 +- 0.664
182 T 1.000** 3.669 +- 0.398
184 E 0.990* 3.642 +- 0.476
232 P 0.615 2.606 +- 1.301
Model 8 vs 7 100.7228380000015
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S7_SFBB1)
Pr(w>1) post mean +- SE for w
7 N 0.999** 3.050
13 R 1.000** 3.051
17 P 0.999** 3.048
46 L 0.996** 3.044
51 F 0.815 2.645
53 E 0.974* 2.995
55 G 0.730 2.452
66 A 0.881 2.790
93 S 1.000** 3.051
94 R 0.980* 3.007
100 I 1.000** 3.051
102 T 1.000** 3.051
119 Q 0.634 2.225
131 Q 0.776 2.551
134 Y 0.545 2.048
148 T 0.831 2.676
149 I 0.617 2.212
163 E 0.947 2.937
166 C 0.989* 3.028
182 T 1.000** 3.051
184 E 0.997** 3.046
212 K 0.747 2.491
232 P 0.871 2.766
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: S7_SFBB1)
Pr(w>1) post mean +- SE for w
7 N 0.999** 2.852 +- 0.502
13 R 1.000** 2.854 +- 0.500
17 P 0.998** 2.851 +- 0.505
46 L 0.996** 2.845 +- 0.513
51 F 0.807 2.381 +- 0.835
53 E 0.971* 2.790 +- 0.590
55 G 0.748 2.258 +- 0.905
65 L 0.567 1.855 +- 0.942
66 A 0.869 2.537 +- 0.782
78 G 0.574 1.873 +- 0.976
93 S 1.000** 2.854 +- 0.500
94 R 0.975* 2.794 +- 0.577
100 I 1.000** 2.854 +- 0.500
102 T 1.000** 2.854 +- 0.500
119 Q 0.672 2.104 +- 0.986
131 Q 0.783 2.343 +- 0.889
134 Y 0.635 1.997 +- 0.915
148 T 0.828 2.444 +- 0.843
149 I 0.677 2.075 +- 0.882
163 E 0.932 2.688 +- 0.670
166 C 0.987* 2.825 +- 0.541
182 T 1.000** 2.855 +- 0.499
184 E 0.997** 2.848 +- 0.510
212 K 0.760 2.280 +- 0.892
232 P 0.863 2.528 +- 0.797
