--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Jan 29 01:35:13 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_5/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -18147.53 -18191.23
2 -18146.35 -18187.48
--------------------------------------
TOTAL -18146.77 -18190.56
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 3.942245 0.022384 3.638059 4.215739 3.941111 1174.10 1203.70 1.000
r(A<->C){all} 0.093571 0.000033 0.082862 0.105052 0.093451 748.07 814.42 1.001
r(A<->G){all} 0.305785 0.000248 0.275658 0.335667 0.305067 330.01 390.89 1.000
r(A<->T){all} 0.044033 0.000017 0.036390 0.052297 0.043863 777.36 873.05 1.000
r(C<->G){all} 0.053617 0.000034 0.041690 0.064154 0.053446 584.54 742.40 1.000
r(C<->T){all} 0.438156 0.000331 0.402588 0.473088 0.438596 364.16 381.95 1.001
r(G<->T){all} 0.064839 0.000038 0.052780 0.076279 0.064797 633.02 666.12 1.000
pi(A){all} 0.409437 0.000096 0.390644 0.427482 0.409388 572.64 750.49 1.000
pi(C){all} 0.191345 0.000063 0.176274 0.207003 0.191176 360.07 466.65 1.000
pi(G){all} 0.220480 0.000060 0.203430 0.234282 0.220425 654.99 676.14 1.000
pi(T){all} 0.178738 0.000059 0.163937 0.193772 0.178506 704.31 850.88 1.000
alpha{1,2} 0.358746 0.000556 0.315129 0.405625 0.357497 779.45 893.38 1.000
alpha{3} 2.558066 0.096526 1.984325 3.203797 2.530884 1341.55 1376.30 1.000
pinvar{all} 0.219938 0.000431 0.181973 0.260970 0.219380 951.50 1017.18 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 -16196.051609
Model 2: PositiveSelection -16129.359473
Model 0: one-ratio -17050.379215
Model 3: discrete -16066.359146
Model 7: beta -16105.451344
Model 8: beta&w>1 -16041.37071
Model 0 vs 1 1708.6552120000015
Model 2 vs 1 133.38427199999933
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: BC.CN.09.1471.KP234768_)
Pr(w>1) post mean +- SE for w
26 K 0.979* 3.142
77 F 0.997** 3.184
89 G 0.707 2.548
117 A 0.580 2.270
138 P 1.000** 3.189
207 L 1.000** 3.189
215 N 0.749 2.639
244 S 1.000** 3.189
272 T 0.999** 3.188
363 G 1.000** 3.189
364 A 0.999** 3.187
454 T 0.998** 3.186
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: BC.CN.09.1471.KP234768_)
Pr(w>1) post mean +- SE for w
26 K 0.978* 3.351 +- 0.458
77 F 0.998** 3.399 +- 0.318
89 G 0.652 2.545 +- 1.160
117 A 0.517 2.211 +- 1.200
138 P 1.000** 3.404 +- 0.298
207 L 1.000** 3.403 +- 0.300
215 N 0.714 2.699 +- 1.110
244 S 1.000** 3.404 +- 0.298
272 T 0.999** 3.403 +- 0.303
363 G 1.000** 3.404 +- 0.298
364 A 0.999** 3.401 +- 0.308
454 T 0.999** 3.401 +- 0.311
Model 8 vs 7 128.16126799999984
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: BC.CN.09.1471.KP234768_)
Pr(w>1) post mean +- SE for w
26 K 0.984* 2.576
77 F 0.998** 2.599
89 G 0.851 2.352
117 A 0.783 2.236
138 P 1.000** 2.602
207 L 1.000** 2.602
215 N 0.875 2.392
244 S 1.000** 2.602
272 T 0.999** 2.602
363 G 1.000** 2.602
364 A 0.999** 2.601
370 S 0.605 1.932
454 T 0.999** 2.600
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: BC.CN.09.1471.KP234768_)
Pr(w>1) post mean +- SE for w
26 K 0.987* 2.484 +- 0.186
77 F 0.998** 2.501 +- 0.094
82 T 0.588 1.850 +- 0.780
89 G 0.892 2.332 +- 0.489
117 A 0.843 2.255 +- 0.572
138 P 1.000** 2.504 +- 0.065
207 L 1.000** 2.504 +- 0.069
215 N 0.908 2.358 +- 0.457
244 S 1.000** 2.504 +- 0.065
272 T 0.999** 2.503 +- 0.074
363 G 1.000** 2.504 +- 0.065
364 A 0.999** 2.503 +- 0.077
370 S 0.707 2.039 +- 0.719
454 T 0.999** 2.503 +- 0.083
