--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sun Mar 18 10:16:48 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_A1/GAG_1_1/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_1_1/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_A1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -17747.97 -17798.50
2 -17751.04 -17799.62
--------------------------------------
TOTAL -17748.62 -17799.21
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_1_1/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_A1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 3.738079 0.018388 3.479724 4.012158 3.737135 888.42 1045.81 1.003
r(A<->C){all} 0.089414 0.000031 0.078181 0.099606 0.089356 669.68 683.54 1.009
r(A<->G){all} 0.287495 0.000221 0.258821 0.316194 0.287047 453.38 476.43 1.004
r(A<->T){all} 0.047975 0.000019 0.039622 0.056101 0.047870 771.16 797.17 1.004
r(C<->G){all} 0.045823 0.000027 0.035820 0.055943 0.045774 706.61 738.61 1.006
r(C<->T){all} 0.469394 0.000317 0.436139 0.505615 0.469824 397.23 440.44 1.010
r(G<->T){all} 0.059898 0.000038 0.047500 0.071745 0.059791 563.99 606.61 1.062
pi(A){all} 0.401985 0.000090 0.384236 0.421298 0.401816 486.78 628.14 1.002
pi(C){all} 0.199067 0.000060 0.183174 0.213420 0.199110 493.84 601.82 1.048
pi(G){all} 0.220966 0.000057 0.205744 0.234911 0.220934 633.51 647.89 1.006
pi(T){all} 0.177982 0.000060 0.163154 0.193371 0.177810 635.65 676.37 1.041
alpha{1,2} 0.340883 0.000561 0.291903 0.384577 0.339862 1113.27 1180.76 1.002
alpha{3} 2.151079 0.074632 1.644252 2.690945 2.131353 1344.51 1345.19 1.002
pinvar{all} 0.205728 0.000535 0.160916 0.250257 0.205579 1025.00 1149.94 1.003
------------------------------------------------------------------------------------------------------
* 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 -16266.313708
Model 2: PositiveSelection -16178.783957
Model 0: one-ratio -17191.380326
Model 3: discrete -16121.113931
Model 7: beta -16191.48603
Model 8: beta&w>1 -16101.849381
Model 0 vs 1 1850.1332359999979
Model 2 vs 1 175.05950200000007
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: CD.NP.11.11NP079.KU341727_)
Pr(w>1) post mean +- SE for w
13 K 0.990** 2.788
26 H 0.999** 2.803
52 S 0.974* 2.759
65 A 0.997** 2.800
77 H 0.985* 2.779
88 A 0.989* 2.786
89 G 1.000** 2.806
91 E 0.733 2.324
113 K 0.785 2.418
114 G 0.778 2.406
126 L 0.700 2.264
134 A 0.988* 2.784
202 L 0.955* 2.726
210 I 1.000** 2.806
239 G 0.998** 2.803
267 V 1.000** 2.806
344 G 0.712 2.286
359 S 1.000** 2.806
360 T 0.999** 2.805
371 S 0.994** 2.796
424 N 0.894 2.615
450 P 1.000** 2.806
457 T 1.000** 2.806
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: CD.NP.11.11NP079.KU341727_)
Pr(w>1) post mean +- SE for w
13 K 0.987* 2.550 +- 0.312
26 H 0.998** 2.570 +- 0.271
52 S 0.966* 2.515 +- 0.379
65 A 0.995** 2.565 +- 0.285
77 H 0.976* 2.536 +- 0.351
82 T 0.510 1.774 +- 0.766
88 A 0.985* 2.547 +- 0.318
89 G 1.000** 2.573 +- 0.261
91 E 0.742 2.130 +- 0.678
113 K 0.792 2.207 +- 0.633
114 G 0.778 2.187 +- 0.650
126 L 0.676 2.041 +- 0.738
134 A 0.980* 2.543 +- 0.338
202 L 0.938 2.473 +- 0.451
210 I 1.000** 2.573 +- 0.263
239 G 0.998** 2.570 +- 0.272
267 V 0.999** 2.573 +- 0.264
344 G 0.706 2.079 +- 0.711
359 S 1.000** 2.573 +- 0.262
360 T 0.999** 2.572 +- 0.266
366 S 0.515 1.780 +- 0.762
371 S 0.991** 2.559 +- 0.300
424 N 0.871 2.355 +- 0.563
450 P 1.000** 2.573 +- 0.261
457 T 1.000** 2.573 +- 0.261
Model 8 vs 7 179.27329800000007
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: CD.NP.11.11NP079.KU341727_)
Pr(w>1) post mean +- SE for w
13 K 0.999** 2.235
18 R 0.507 1.519
26 H 1.000** 2.237
52 S 0.995** 2.231
65 A 0.999** 2.236
77 H 0.996** 2.232
82 T 0.831 1.993
88 A 0.998** 2.234
89 G 1.000** 2.237
91 E 0.945 2.158
113 K 0.961* 2.182
114 G 0.955* 2.173
126 L 0.896 2.088
134 A 0.997** 2.233
202 L 0.988* 2.220
210 I 1.000** 2.237
239 G 1.000** 2.237
267 V 1.000** 2.237
344 G 0.927 2.132
359 S 1.000** 2.237
360 T 1.000** 2.237
366 S 0.835 2.000
371 S 0.998** 2.235
424 N 0.972* 2.197
450 P 1.000** 2.237
457 T 1.000** 2.237
468 L 0.589 1.633
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: CD.NP.11.11NP079.KU341727_)
Pr(w>1) post mean +- SE for w
13 K 0.986* 2.478 +- 0.184
26 H 0.998** 2.497 +- 0.073
52 S 0.975* 2.461 +- 0.246
65 A 0.997** 2.496 +- 0.079
77 H 0.987* 2.480 +- 0.178
82 T 0.563 1.803 +- 0.793
88 A 0.984* 2.475 +- 0.197
89 G 1.000** 2.500 +- 0.003
91 E 0.728 2.071 +- 0.702
113 K 0.757 2.118 +- 0.675
114 G 0.772 2.141 +- 0.662
126 L 0.720 2.053 +- 0.717
134 A 0.991** 2.485 +- 0.152
202 L 0.959* 2.435 +- 0.313
210 I 1.000** 2.500 +- 0.021
239 G 0.998** 2.497 +- 0.069
267 V 1.000** 2.500 +- 0.025
344 G 0.737 2.083 +- 0.699
359 S 1.000** 2.500 +- 0.025
360 T 0.999** 2.499 +- 0.043
366 S 0.534 1.759 +- 0.795
371 S 0.993** 2.490 +- 0.128
424 N 0.889 2.325 +- 0.497
450 P 1.000** 2.500 +- 0.001
457 T 1.000** 2.500 +- 0.007
