--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Dec 02 22:49:08 WET 2016
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=/opt/ADOPS/85/CG15822-PG/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/85/CG15822-PG/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/85/CG15822-PG/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/ADOPS/85/CG15822-PG/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -15778.15 -15793.52
2 -15777.77 -15793.97
--------------------------------------
TOTAL -15777.94 -15793.77
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/85/CG15822-PG/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/85/CG15822-PG/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/ADOPS/85/CG15822-PG/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.123199 0.001954 1.036276 1.207578 1.121198 1223.19 1302.27 1.000
r(A<->C){all} 0.106953 0.000073 0.090548 0.123605 0.106671 988.32 989.48 1.000
r(A<->G){all} 0.253741 0.000200 0.224834 0.280489 0.253666 913.84 924.36 1.001
r(A<->T){all} 0.100279 0.000102 0.079559 0.118974 0.099839 984.77 1033.52 1.001
r(C<->G){all} 0.075287 0.000040 0.063225 0.088279 0.075254 1015.29 1033.14 1.000
r(C<->T){all} 0.401858 0.000290 0.368504 0.435083 0.401580 825.37 874.72 1.000
r(G<->T){all} 0.061883 0.000048 0.048795 0.075169 0.061826 786.29 883.60 1.001
pi(A){all} 0.228295 0.000038 0.216492 0.240658 0.228237 778.32 802.50 1.000
pi(C){all} 0.285774 0.000044 0.273315 0.298624 0.285823 991.61 1018.75 1.000
pi(G){all} 0.301789 0.000045 0.288194 0.314498 0.301844 1183.55 1184.64 1.001
pi(T){all} 0.184142 0.000031 0.172799 0.194450 0.184160 920.44 1081.27 1.001
alpha{1,2} 0.217141 0.000228 0.189676 0.248082 0.216458 1161.13 1264.81 1.000
alpha{3} 4.126773 0.715178 2.626800 5.848609 4.021962 1274.90 1387.95 1.000
pinvar{all} 0.380077 0.000475 0.337407 0.421851 0.380431 1141.89 1275.68 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 -14278.364164
Model 2: PositiveSelection -14278.364165
Model 0: one-ratio -14586.342621
Model 3: discrete -14254.990939
Model 7: beta -14261.142299
Model 8: beta&w>1 -14255.199834
Model 0 vs 1 615.9569139999985
Model 2 vs 1 2.0000006770715117E-6
Model 8 vs 7 11.884930000000168
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_CG15822-PG)
Pr(w>1) post mean +- SE for w
247 G 0.641 1.343
254 G 0.930 1.702
795 A 0.871 1.629
798 S 0.895 1.658
881 S 0.980* 1.764
969 L 0.703 1.420
1018 N 0.611 1.305
1026 G 0.685 1.397
1182 L 0.967* 1.748
1197 T 0.649 1.351
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: D_melanogaster_CG15822-PG)
Pr(w>1) post mean +- SE for w
173 A 0.524 1.011 +- 0.535
247 G 0.920 1.434 +- 0.229
252 S 0.666 1.170 +- 0.484
253 A 0.776 1.285 +- 0.412
254 G 0.977* 1.482 +- 0.117
377 S 0.795 1.311 +- 0.382
380 M 0.817 1.343 +- 0.339
518 H 0.555 1.071 +- 0.497
607 P 0.797 1.314 +- 0.378
609 R 0.726 1.254 +- 0.413
610 S 0.718 1.224 +- 0.455
612 S 0.627 1.145 +- 0.476
614 S 0.748 1.274 +- 0.400
767 Q 0.749 1.274 +- 0.401
784 V 0.666 1.184 +- 0.461
787 G 0.530 1.022 +- 0.530
788 E 0.700 1.219 +- 0.443
789 N 0.872 1.389 +- 0.296
795 A 0.965* 1.473 +- 0.145
796 A 0.876 1.393 +- 0.291
797 Y 0.741 1.260 +- 0.418
798 S 0.969* 1.475 +- 0.141
807 S 0.593 1.110 +- 0.487
836 G 0.553 1.068 +- 0.499
838 G 0.593 1.090 +- 0.515
870 L 0.508 0.996 +- 0.536
881 S 0.990* 1.492 +- 0.076
946 C 0.625 1.144 +- 0.475
964 I 0.584 1.079 +- 0.519
969 L 0.932 1.444 +- 0.211
1016 V 0.769 1.293 +- 0.387
1018 N 0.912 1.426 +- 0.243
1021 S 0.699 1.227 +- 0.428
1026 G 0.926 1.438 +- 0.224
1101 P 0.854 1.371 +- 0.321
1119 R 0.611 1.110 +- 0.509
1182 L 0.985* 1.489 +- 0.091
1183 A 0.688 1.207 +- 0.450
1197 T 0.914 1.425 +- 0.250
