--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Tue Mar 20 06:56:20 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_A1/GAG_1_5/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -18327.21 -18371.35
2 -18328.67 -18370.91
--------------------------------------
TOTAL -18327.69 -18371.15
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/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} 3.935858 0.019342 3.659284 4.208033 3.934342 802.94 953.12 1.001
r(A<->C){all} 0.091202 0.000032 0.080702 0.102607 0.091094 625.31 741.28 1.000
r(A<->G){all} 0.312617 0.000242 0.282560 0.341310 0.312783 425.33 432.79 1.000
r(A<->T){all} 0.045048 0.000017 0.036403 0.052688 0.044911 833.07 840.70 1.001
r(C<->G){all} 0.048697 0.000026 0.038817 0.057999 0.048721 599.23 717.89 1.000
r(C<->T){all} 0.428210 0.000306 0.395412 0.463020 0.428166 402.35 415.21 1.000
r(G<->T){all} 0.074225 0.000043 0.061397 0.086894 0.073858 635.35 738.43 1.000
pi(A){all} 0.398270 0.000084 0.380658 0.416867 0.398367 611.99 737.75 1.000
pi(C){all} 0.206623 0.000065 0.191095 0.222220 0.206496 477.62 519.09 1.000
pi(G){all} 0.214060 0.000060 0.199768 0.229666 0.214065 562.29 621.94 1.000
pi(T){all} 0.181047 0.000057 0.166452 0.195647 0.180959 693.59 749.56 1.000
alpha{1,2} 0.300114 0.000378 0.263201 0.337521 0.299038 1048.79 1189.67 1.000
alpha{3} 1.736297 0.040599 1.361735 2.131270 1.724120 1168.17 1203.51 1.001
pinvar{all} 0.149418 0.000584 0.101102 0.195927 0.149388 1075.33 1103.82 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 -15275.88814
Model 2: PositiveSelection -15214.968097
Model 0: one-ratio -16149.492641
Model 3: discrete -15140.327268
Model 7: beta -15179.162644
Model 8: beta&w>1 -15120.366518
Model 0 vs 1 1747.2090020000032
Model 2 vs 1 121.84008599999652
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.TH.00.C015F1P190.GU458453_)
Pr(w>1) post mean +- SE for w
28 Q 0.774 2.461
59 I 0.984* 2.858
65 T 0.982* 2.854
77 Y 0.985* 2.860
82 T 1.000** 2.888
89 R 1.000** 2.888
91 D 0.608 2.148
129 S 0.999** 2.887
198 V 0.999** 2.887
206 I 0.976* 2.842
235 S 1.000** 2.888
354 A 0.949 2.792
355 N 1.000** 2.887
441 V 0.758 2.431
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.TH.00.C015F1P190.GU458453_)
Pr(w>1) post mean +- SE for w
28 Q 0.753 2.218 +- 0.750
59 I 0.979* 2.707 +- 0.491
65 T 0.978* 2.711 +- 0.498
77 Y 0.982* 2.718 +- 0.487
82 T 1.000** 2.749 +- 0.433
89 R 1.000** 2.749 +- 0.433
91 D 0.630 2.000 +- 0.798
129 S 0.999** 2.748 +- 0.436
198 V 0.999** 2.748 +- 0.435
206 I 0.971* 2.696 +- 0.514
235 S 1.000** 2.749 +- 0.433
354 A 0.937 2.617 +- 0.584
355 N 0.999** 2.748 +- 0.435
441 V 0.746 2.253 +- 0.803
Model 8 vs 7 117.59225199999855
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.TH.00.C015F1P190.GU458453_)
Pr(w>1) post mean +- SE for w
28 Q 0.923 2.200
59 I 0.993** 2.303
65 T 0.992** 2.301
77 Y 0.993** 2.302
82 T 1.000** 2.312
89 R 1.000** 2.312
91 D 0.842 2.082
129 S 1.000** 2.312
198 V 1.000** 2.312
206 I 0.990* 2.298
235 S 1.000** 2.312
354 A 0.983* 2.287
355 N 1.000** 2.312
441 V 0.903 2.171
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.TH.00.C015F1P190.GU458453_)
Pr(w>1) post mean +- SE for w
28 Q 0.833 2.238 +- 0.585
59 I 0.988* 2.481 +- 0.173
65 T 0.991** 2.486 +- 0.150
77 Y 0.992** 2.487 +- 0.143
82 T 1.000** 2.500 +- 0.006
89 R 1.000** 2.500 +- 0.015
91 D 0.734 2.081 +- 0.697
129 S 1.000** 2.499 +- 0.030
198 V 1.000** 2.499 +- 0.032
206 I 0.986* 2.477 +- 0.187
235 S 1.000** 2.500 +- 0.003
354 A 0.967* 2.448 +- 0.280
355 N 1.000** 2.499 +- 0.030
441 V 0.872 2.297 +- 0.530
