--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Jan 27 19:14:20 WET 2018
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=/usr/bin/
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb
tcoffee.bin=t_coffee
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/HIV1_N1/GAG_1_2/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_2/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/HIV1_N1/GAG_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -17418.94 -17467.06
2 -17416.52 -17465.71
--------------------------------------
TOTAL -17417.13 -17466.60
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_2/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/HIV1_N1/GAG_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 3.664582 0.017174 3.415009 3.920539 3.661478 1363.17 1390.21 1.000
r(A<->C){all} 0.085815 0.000029 0.075024 0.095867 0.085780 699.61 731.79 1.000
r(A<->G){all} 0.325048 0.000258 0.294321 0.356344 0.324665 417.94 443.89 1.001
r(A<->T){all} 0.047500 0.000017 0.039042 0.055214 0.047451 580.17 764.70 1.001
r(C<->G){all} 0.045901 0.000027 0.035866 0.055888 0.045822 569.97 690.70 1.000
r(C<->T){all} 0.429957 0.000315 0.394593 0.463562 0.430299 399.84 448.78 1.001
r(G<->T){all} 0.065779 0.000040 0.054040 0.079132 0.065706 664.68 778.67 1.001
pi(A){all} 0.414011 0.000091 0.395456 0.432463 0.413935 733.21 788.57 1.000
pi(C){all} 0.196870 0.000060 0.181473 0.211808 0.196789 647.45 727.51 1.003
pi(G){all} 0.211998 0.000059 0.196424 0.225968 0.211954 397.34 552.99 1.004
pi(T){all} 0.177121 0.000053 0.163057 0.191572 0.177010 529.57 625.78 1.000
alpha{1,2} 0.316913 0.000474 0.275851 0.361655 0.316001 941.95 1078.66 1.000
alpha{3} 2.280095 0.089029 1.745101 2.915918 2.261138 1244.40 1329.12 1.000
pinvar{all} 0.177769 0.000546 0.128612 0.219657 0.177672 947.50 1073.38 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 -15746.913577
Model 2: PositiveSelection -15685.569871
Model 0: one-ratio -16603.611266
Model 3: discrete -15606.785351
Model 7: beta -15645.983528
Model 8: beta&w>1 -15582.541691
Model 0 vs 1 1713.395378000001
Model 2 vs 1 122.68741199999931
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 01_AE.CM.07.BS65.JX244941_)
Pr(w>1) post mean +- SE for w
13 A 0.635 2.046
26 K 0.988* 2.626
29 L 0.746 2.229
65 A 0.845 2.392
77 Y 0.999** 2.645
82 T 0.997** 2.641
88 Q 0.877 2.444
89 R 1.000** 2.647
91 E 0.763 2.256
125 T 0.829 2.366
133 P 1.000** 2.646
202 V 0.977* 2.608
210 N 0.987* 2.625
229 N 0.512 1.843
239 S 1.000** 2.647
344 S 0.913 2.503
359 Q 1.000** 2.646
360 G 0.612 2.008
434 S 0.878 2.446
454 V 0.999** 2.646
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: 01_AE.CM.07.BS65.JX244941_)
Pr(w>1) post mean +- SE for w
13 A 0.651 1.977 +- 0.716
26 K 0.984* 2.485 +- 0.214
29 L 0.723 2.087 +- 0.675
65 A 0.811 2.223 +- 0.595
77 Y 0.999** 2.508 +- 0.112
82 T 0.995** 2.502 +- 0.146
88 Q 0.864 2.300 +- 0.520
89 R 1.000** 2.510 +- 0.099
91 E 0.748 2.124 +- 0.655
125 T 0.798 2.202 +- 0.610
133 P 1.000** 2.509 +- 0.103
202 V 0.968* 2.462 +- 0.282
210 N 0.981* 2.482 +- 0.225
239 S 1.000** 2.510 +- 0.100
344 S 0.893 2.347 +- 0.473
359 Q 1.000** 2.510 +- 0.101
360 G 0.590 1.887 +- 0.740
434 S 0.862 2.297 +- 0.524
454 V 0.999** 2.509 +- 0.108
Model 8 vs 7 126.88367400000061
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 01_AE.CM.07.BS65.JX244941_)
Pr(w>1) post mean +- SE for w
13 A 0.946 1.987
26 K 0.998** 2.051
28 K 0.796 1.800
29 L 0.937 1.975
65 A 0.964* 2.009
73 V 0.756 1.745
77 Y 1.000** 2.054
82 T 0.999** 2.053
88 Q 0.978* 2.027
89 R 1.000** 2.054
91 E 0.953* 1.996
111 D 0.656 1.622
114 H 0.820 1.829
125 T 0.961* 2.005
133 P 1.000** 2.054
134 L 0.760 1.756
202 V 0.995** 2.048
210 N 0.997** 2.051
229 N 0.848 1.864
239 S 1.000** 2.054
267 V 0.545 1.477
344 S 0.982* 2.032
359 Q 1.000** 2.054
360 G 0.901 1.930
374 I 0.757 1.750
434 S 0.978* 2.027
454 V 1.000** 2.054
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: 01_AE.CM.07.BS65.JX244941_)
Pr(w>1) post mean +- SE for w
13 A 0.533 1.767 +- 0.785
26 K 0.986* 2.479 +- 0.181
29 L 0.720 2.057 +- 0.711
65 A 0.892 2.329 +- 0.492
73 V 0.523 1.729 +- 0.811
77 Y 1.000** 2.499 +- 0.032
82 T 0.998** 2.497 +- 0.073
88 Q 0.840 2.249 +- 0.576
89 R 1.000** 2.500 +- 0.001
91 E 0.730 2.074 +- 0.701
125 T 0.863 2.283 +- 0.545
133 P 1.000** 2.500 +- 0.017
202 V 0.982* 2.471 +- 0.212
210 N 0.989* 2.483 +- 0.162
229 N 0.582 1.832 +- 0.790
239 S 1.000** 2.500 +- 0.011
344 S 0.927 2.385 +- 0.410
359 Q 1.000** 2.500 +- 0.015
360 G 0.620 1.897 +- 0.771
434 S 0.872 2.298 +- 0.527
454 V 1.000** 2.499 +- 0.029
