--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Jan 27 09:17:35 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_1/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/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_N1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -18272.33 -18319.14
2 -18273.56 -18313.19
--------------------------------------
TOTAL -18272.77 -18318.45
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/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_N1/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} 3.935340 0.019459 3.659520 4.203024 3.935345 1223.88 1300.51 1.000
r(A<->C){all} 0.087036 0.000029 0.077142 0.098518 0.086923 708.97 716.90 1.000
r(A<->G){all} 0.309475 0.000224 0.279997 0.337671 0.309110 296.43 386.32 1.000
r(A<->T){all} 0.045167 0.000017 0.037245 0.053086 0.045104 667.74 836.36 1.000
r(C<->G){all} 0.043314 0.000025 0.033523 0.052731 0.043060 565.03 718.61 1.000
r(C<->T){all} 0.435891 0.000308 0.400834 0.467960 0.436154 307.19 373.02 1.000
r(G<->T){all} 0.079117 0.000048 0.065913 0.092391 0.079029 614.51 669.83 1.000
pi(A){all} 0.398392 0.000080 0.381733 0.416692 0.398541 763.25 774.72 1.000
pi(C){all} 0.205047 0.000057 0.190982 0.220586 0.204874 534.57 687.05 1.000
pi(G){all} 0.218028 0.000061 0.203262 0.233594 0.217976 532.13 591.87 1.000
pi(T){all} 0.178532 0.000051 0.163902 0.191875 0.178439 476.21 599.20 1.000
alpha{1,2} 0.342905 0.000510 0.297558 0.384129 0.341400 1003.47 1088.03 1.000
alpha{3} 1.906849 0.051151 1.461061 2.325904 1.897151 1414.61 1433.47 1.000
pinvar{all} 0.162694 0.000527 0.117398 0.206237 0.163032 958.43 1067.22 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 -16324.941755
Model 2: PositiveSelection -16268.105319
Model 0: one-ratio -17178.663071
Model 3: discrete -16203.783623
Model 7: beta -16231.126789
Model 8: beta&w>1 -16173.827495
Model 0 vs 1 1707.4426319999984
Model 2 vs 1 113.67287199999919
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.07.07CNYN367.KF835544_)
Pr(w>1) post mean +- SE for w
77 Y 0.973* 2.688
82 T 1.000** 2.734
89 G 0.999** 2.733
91 E 0.854 2.481
115 T 1.000** 2.735
134 P 0.993** 2.723
201 T 0.987* 2.712
209 V 0.920 2.595
238 S 1.000** 2.734
358 S 1.000** 2.734
359 A 0.987* 2.713
370 P 0.530 1.919
424 H 0.778 2.350
445 S 0.725 2.258
451 P 0.998** 2.731
455 P 0.986* 2.711
457 L 0.572 1.993
458 T 0.580 2.006
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.07.07CNYN367.KF835544_)
Pr(w>1) post mean +- SE for w
77 Y 0.968* 2.469 +- 0.299
82 T 1.000** 2.518 +- 0.134
89 G 0.999** 2.517 +- 0.143
91 E 0.874 2.320 +- 0.510
115 T 1.000** 2.518 +- 0.134
116 I 0.529 1.797 +- 0.755
134 P 0.991** 2.504 +- 0.196
201 T 0.983* 2.493 +- 0.235
209 V 0.919 2.393 +- 0.430
238 S 0.999** 2.517 +- 0.139
358 S 1.000** 2.518 +- 0.137
359 A 0.985* 2.496 +- 0.225
370 P 0.561 1.846 +- 0.751
424 H 0.797 2.203 +- 0.615
445 S 0.754 2.138 +- 0.654
451 P 0.997** 2.514 +- 0.156
455 P 0.982* 2.491 +- 0.242
457 L 0.606 1.913 +- 0.740
458 T 0.613 1.925 +- 0.737
Model 8 vs 7 114.59858800000075
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.07.07CNYN367.KF835544_)
Pr(w>1) post mean +- SE for w
13 K 0.692 1.767
65 A 0.517 1.527
77 Y 0.988* 2.148
82 T 1.000** 2.163
89 G 1.000** 2.162
91 E 0.954* 2.104
115 T 1.000** 2.163
116 I 0.771 1.864
126 L 0.685 1.754
134 P 0.997** 2.159
201 T 0.993** 2.154
209 V 0.971* 2.125
238 S 1.000** 2.163
266 T 0.547 1.567
358 S 1.000** 2.163
359 A 0.994** 2.156
370 P 0.746 1.831
424 H 0.914 2.051
445 S 0.900 2.033
451 P 0.999** 2.161
455 P 0.993** 2.153
457 L 0.812 1.919
458 T 0.832 1.944
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.07.07CNYN367.KF835544_)
Pr(w>1) post mean +- SE for w
77 Y 0.982* 2.471 +- 0.212
82 T 1.000** 2.500 +- 0.007
89 G 0.999** 2.499 +- 0.042
91 E 0.865 2.288 +- 0.536
115 T 1.000** 2.500 +- 0.005
116 I 0.618 1.892 +- 0.774
134 P 0.996** 2.494 +- 0.099
201 T 0.990* 2.484 +- 0.158
209 V 0.938 2.403 +- 0.378
238 S 1.000** 2.499 +- 0.031
358 S 1.000** 2.500 +- 0.025
359 A 0.989* 2.483 +- 0.163
370 P 0.576 1.826 +- 0.788
424 H 0.809 2.199 +- 0.620
445 S 0.775 2.145 +- 0.659
451 P 0.999** 2.498 +- 0.058
455 P 0.990* 2.484 +- 0.157
457 L 0.658 1.958 +- 0.753
458 T 0.692 2.011 +- 0.733
