--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Mar 19 09:39:02 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_3/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -18336.02 -18377.73
2 -18334.19 -18377.40
--------------------------------------
TOTAL -18334.74 -18377.58
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 4.026504 0.019969 3.752870 4.299663 4.023954 1175.84 1338.42 1.000
r(A<->C){all} 0.088545 0.000029 0.077834 0.098794 0.088426 730.02 799.71 1.001
r(A<->G){all} 0.290144 0.000218 0.261671 0.318327 0.289661 404.25 435.77 1.000
r(A<->T){all} 0.045460 0.000018 0.037590 0.053881 0.045224 653.07 763.55 1.000
r(C<->G){all} 0.049818 0.000029 0.039570 0.060784 0.049794 619.70 735.89 1.001
r(C<->T){all} 0.470715 0.000295 0.438789 0.503835 0.470604 396.65 426.23 1.000
r(G<->T){all} 0.055318 0.000031 0.045161 0.066733 0.055182 682.92 709.87 1.001
pi(A){all} 0.409405 0.000091 0.391819 0.429154 0.409359 610.67 716.82 1.000
pi(C){all} 0.192988 0.000055 0.178283 0.207081 0.193025 572.17 584.13 1.000
pi(G){all} 0.218744 0.000060 0.204618 0.234338 0.218596 581.92 657.23 1.001
pi(T){all} 0.178863 0.000054 0.165255 0.193645 0.178690 550.52 603.91 1.000
alpha{1,2} 0.334030 0.000478 0.292183 0.375795 0.332230 1203.79 1243.41 1.001
alpha{3} 2.223434 0.069419 1.729036 2.743273 2.203580 1313.74 1368.45 1.000
pinvar{all} 0.190207 0.000458 0.148178 0.232520 0.190282 956.31 1042.92 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 -16205.491699
Model 2: PositiveSelection -16120.60129
Model 0: one-ratio -17104.802154
Model 3: discrete -16055.996365
Model 7: beta -16113.182856
Model 8: beta&w>1 -16034.032634
Model 0 vs 1 1798.6209100000015
Model 2 vs 1 169.78081799999927
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.ZA.06.CAP040_2_01.JF704683_)
Pr(w>1) post mean +- SE for w
13 K 0.975* 2.915
77 F 1.000** 2.963
82 T 0.502 1.986
89 K 1.000** 2.963
91 E 0.805 2.581
115 A 0.997** 2.958
116 D 0.969* 2.903
135 A 0.999** 2.961
204 L 0.998** 2.960
212 V 0.959* 2.883
241 S 1.000** 2.963
269 V 0.998** 2.959
292 C 0.976* 2.916
346 S 0.509 1.999
361 S 0.969* 2.902
449 T 1.000** 2.963
450 Q 0.937 2.840
454 P 1.000** 2.963
455 T 0.968* 2.900
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: C.ZA.06.CAP040_2_01.JF704683_)
Pr(w>1) post mean +- SE for w
13 K 0.933 3.110 +- 0.700
77 F 1.000** 3.274 +- 0.419
89 K 1.000** 3.274 +- 0.418
91 E 0.564 2.210 +- 1.123
115 A 0.996** 3.265 +- 0.443
116 D 0.932 3.111 +- 0.702
135 A 0.998** 3.271 +- 0.427
204 L 0.998** 3.270 +- 0.430
212 V 0.924 3.092 +- 0.727
241 S 1.000** 3.274 +- 0.418
269 V 0.997** 3.267 +- 0.437
292 C 0.959* 3.178 +- 0.610
361 S 0.924 3.091 +- 0.725
449 T 1.000** 3.274 +- 0.418
450 Q 0.904 3.051 +- 0.779
454 P 1.000** 3.274 +- 0.418
455 T 0.944 3.143 +- 0.662
Model 8 vs 7 158.30044400000043
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.ZA.06.CAP040_2_01.JF704683_)
Pr(w>1) post mean +- SE for w
13 K 0.991** 2.324
26 H 0.563 1.689
28 M 0.785 2.019
65 A 0.762 1.982
77 F 1.000** 2.336
82 T 0.772 1.997
89 K 1.000** 2.337
91 E 0.930 2.234
115 A 0.999** 2.335
116 D 0.987* 2.318
127 L 0.517 1.609
135 A 0.999** 2.336
204 L 0.999** 2.335
212 V 0.984* 2.313
241 S 1.000** 2.337
269 V 0.999** 2.335
292 C 0.990** 2.323
346 S 0.776 2.004
361 S 0.986* 2.316
449 T 1.000** 2.337
450 Q 0.969* 2.291
454 P 1.000** 2.337
455 T 0.987* 2.317
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: C.ZA.06.CAP040_2_01.JF704683_)
Pr(w>1) post mean +- SE for w
13 K 0.976* 2.462 +- 0.241
28 M 0.532 1.764 +- 0.785
65 A 0.661 1.959 +- 0.757
77 F 1.000** 2.500 +- 0.022
82 T 0.659 1.957 +- 0.756
89 K 1.000** 2.500 +- 0.005
91 E 0.840 2.249 +- 0.576
115 A 0.997** 2.496 +- 0.083
116 D 0.972* 2.456 +- 0.260
135 A 0.999** 2.498 +- 0.053
204 L 0.998** 2.497 +- 0.063
212 V 0.970* 2.452 +- 0.271
241 S 1.000** 2.500 +- 0.008
269 V 0.998** 2.497 +- 0.070
292 C 0.983* 2.473 +- 0.206
346 S 0.636 1.923 +- 0.764
361 S 0.968* 2.450 +- 0.277
449 T 1.000** 2.500 +- 0.003
450 Q 0.953* 2.426 +- 0.335
454 P 1.000** 2.500 +- 0.001
455 T 0.977* 2.464 +- 0.236
