--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sun Mar 18 20:09:30 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_2/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/GAG_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -18206.01 -18254.40
2 -18207.59 -18246.56
--------------------------------------
TOTAL -18206.52 -18253.71
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/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} 3.983994 0.021438 3.697997 4.267852 3.976770 1066.53 1283.76 1.001
r(A<->C){all} 0.085041 0.000028 0.074685 0.095448 0.084916 675.73 793.44 1.000
r(A<->G){all} 0.319159 0.000249 0.290947 0.350971 0.318175 357.41 390.40 1.001
r(A<->T){all} 0.046581 0.000017 0.038670 0.054498 0.046408 701.22 758.23 1.000
r(C<->G){all} 0.041077 0.000026 0.031769 0.050930 0.040758 695.53 782.73 1.000
r(C<->T){all} 0.439626 0.000328 0.404604 0.474526 0.440259 309.37 325.22 1.001
r(G<->T){all} 0.068516 0.000038 0.056344 0.080115 0.068229 571.56 629.52 1.002
pi(A){all} 0.409805 0.000091 0.392203 0.429059 0.409576 535.24 583.38 1.000
pi(C){all} 0.197131 0.000060 0.181389 0.211954 0.197079 340.52 498.03 1.002
pi(G){all} 0.215204 0.000059 0.199257 0.229037 0.215131 720.07 726.72 1.001
pi(T){all} 0.177860 0.000057 0.162515 0.192071 0.177837 476.64 542.11 1.000
alpha{1,2} 0.343604 0.000489 0.303144 0.390002 0.342420 1128.72 1182.68 1.000
alpha{3} 2.546157 0.096005 2.003452 3.184145 2.526445 1331.98 1416.49 1.000
pinvar{all} 0.215772 0.000447 0.173894 0.255783 0.215964 1002.77 1062.29 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 -16064.518238
Model 2: PositiveSelection -16002.60006
Model 0: one-ratio -16916.718183
Model 3: discrete -15900.458993
Model 7: beta -15942.618995
Model 8: beta&w>1 -15887.32193
Model 0 vs 1 1704.3998900000006
Model 2 vs 1 123.8363559999998
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 0107.CN.07.JL070032.KC990127_)
Pr(w>1) post mean +- SE for w
13 V 0.996** 3.083
77 F 0.964* 3.018
82 V 1.000** 3.092
89 R 0.992** 3.076
138 P 1.000** 3.092
214 I 0.995** 3.081
243 N 1.000** 3.092
271 V 0.941 2.968
348 S 0.884 2.850
363 Q 1.000** 3.092
364 N 0.996** 3.084
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: 0107.CN.07.JL070032.KC990127_)
Pr(w>1) post mean +- SE for w
13 V 0.995** 3.192 +- 0.481
77 F 0.967* 3.130 +- 0.596
82 V 1.000** 3.202 +- 0.457
89 R 0.993** 3.187 +- 0.492
138 P 1.000** 3.202 +- 0.457
214 I 0.995** 3.191 +- 0.482
243 N 1.000** 3.202 +- 0.458
271 V 0.942 3.071 +- 0.679
348 S 0.876 2.911 +- 0.842
363 Q 1.000** 3.202 +- 0.457
364 N 0.996** 3.195 +- 0.475
Model 8 vs 7 110.59413000000131
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 0107.CN.07.JL070032.KC990127_)
Pr(w>1) post mean +- SE for w
13 V 0.996** 2.390
67 K 0.623 1.824
77 F 0.975* 2.359
82 V 1.000** 2.396
89 R 0.993** 2.385
138 P 1.000** 2.396
214 I 0.995** 2.389
243 N 1.000** 2.396
271 V 0.966* 2.345
348 S 0.925 2.282
363 Q 1.000** 2.396
364 N 0.997** 2.391
453 V 0.578 1.757
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: 0107.CN.07.JL070032.KC990127_)
Pr(w>1) post mean +- SE for w
13 V 0.996** 2.493 +- 0.102
67 K 0.682 1.993 +- 0.743
77 F 0.982* 2.471 +- 0.211
82 V 1.000** 2.500 +- 0.005
89 R 0.994** 2.491 +- 0.121
138 P 1.000** 2.500 +- 0.009
214 I 0.996** 2.494 +- 0.096
243 N 1.000** 2.500 +- 0.017
271 V 0.974* 2.458 +- 0.253
348 S 0.938 2.402 +- 0.380
363 Q 1.000** 2.500 +- 0.009
364 N 0.997** 2.496 +- 0.082
453 V 0.626 1.905 +- 0.771
464 L 0.568 1.802 +- 0.803
