--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Mar 19 21:09:11 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_4/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_1_4/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_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -18505.51 -18545.46
2 -18502.76 -18550.25
--------------------------------------
TOTAL -18503.40 -18549.56
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_1_4/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_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 3.916369 0.017075 3.632718 4.149444 3.913813 1501.00 1501.00 1.001
r(A<->C){all} 0.086823 0.000029 0.076822 0.097348 0.086778 688.01 718.36 1.000
r(A<->G){all} 0.318617 0.000226 0.289993 0.348008 0.318468 285.59 406.09 1.000
r(A<->T){all} 0.050718 0.000018 0.042162 0.058523 0.050529 686.83 784.26 1.000
r(C<->G){all} 0.043157 0.000024 0.033675 0.052712 0.042958 686.75 695.18 1.000
r(C<->T){all} 0.443194 0.000282 0.410512 0.474548 0.443134 307.95 409.52 1.000
r(G<->T){all} 0.057492 0.000032 0.046489 0.068528 0.057246 778.53 839.42 1.001
pi(A){all} 0.405850 0.000089 0.388685 0.425482 0.405577 450.36 557.75 1.000
pi(C){all} 0.198091 0.000059 0.182045 0.212113 0.197985 357.13 510.46 1.000
pi(G){all} 0.222202 0.000059 0.206436 0.236589 0.222089 560.12 597.37 1.000
pi(T){all} 0.173857 0.000053 0.159562 0.187708 0.173760 646.29 696.25 1.000
alpha{1,2} 0.299064 0.000373 0.261232 0.336160 0.297900 1081.55 1182.31 1.000
alpha{3} 1.836839 0.048089 1.427314 2.271389 1.824914 1399.82 1412.65 1.000
pinvar{all} 0.153344 0.000546 0.109483 0.203360 0.153389 1075.73 1196.84 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 -16269.578845
Model 2: PositiveSelection -16208.112831
Model 0: one-ratio -17249.075527
Model 3: discrete -16141.0638
Model 7: beta -16174.633061
Model 8: beta&w>1 -16117.384529
Model 0 vs 1 1958.9933640000017
Model 2 vs 1 122.93202799999926
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: F1.BR.07.07BR844.FJ771010_)
Pr(w>1) post mean +- SE for w
26 K 0.722 2.281
67 Q 0.762 2.352
73 L 0.613 2.088
77 Y 0.998** 2.770
82 V 0.999** 2.773
89 K 0.989* 2.755
129 S 1.000** 2.775
198 L 0.998** 2.770
235 S 0.906 2.609
263 V 1.000** 2.774
340 S 0.777 2.378
355 T 0.998** 2.771
356 A 0.999** 2.773
419 H 0.818 2.451
443 Q 1.000** 2.774
447 A 0.998** 2.770
458 E 0.980* 2.739
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: F1.BR.07.07BR844.FJ771010_)
Pr(w>1) post mean +- SE for w
26 K 0.737 2.133 +- 0.696
67 Q 0.753 2.166 +- 0.695
73 L 0.598 1.926 +- 0.777
77 Y 0.996** 2.570 +- 0.281
82 V 0.998** 2.573 +- 0.272
89 K 0.986* 2.554 +- 0.320
129 S 1.000** 2.576 +- 0.264
198 L 0.997** 2.570 +- 0.280
206 I 0.537 1.816 +- 0.765
235 S 0.900 2.398 +- 0.514
263 V 1.000** 2.575 +- 0.266
340 S 0.775 2.196 +- 0.667
354 N 0.510 1.772 +- 0.763
355 T 0.997** 2.571 +- 0.276
356 A 0.999** 2.574 +- 0.270
419 H 0.810 2.256 +- 0.638
443 Q 1.000** 2.575 +- 0.265
447 A 0.997** 2.570 +- 0.280
458 E 0.972* 2.532 +- 0.369
Model 8 vs 7 114.49706399999923
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: F1.BR.07.07BR844.FJ771010_)
Pr(w>1) post mean +- SE for w
26 K 0.856 2.002
67 Q 0.874 2.024
73 L 0.768 1.884
77 Y 0.998** 2.184
82 V 0.999** 2.185
89 K 0.992** 2.176
129 S 1.000** 2.186
198 L 0.998** 2.184
206 I 0.747 1.861
235 S 0.956* 2.131
263 V 1.000** 2.186
286 T 0.520 1.565
340 S 0.902 2.061
353 T 0.516 1.566
354 N 0.705 1.807
355 T 0.999** 2.184
356 A 0.999** 2.185
419 H 0.904 2.064
443 Q 1.000** 2.186
447 A 0.998** 2.184
458 E 0.986* 2.169
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: F1.BR.07.07BR844.FJ771010_)
Pr(w>1) post mean +- SE for w
26 K 0.771 2.140 +- 0.661
67 Q 0.836 2.240 +- 0.587
73 L 0.734 2.074 +- 0.710
77 Y 0.999** 2.498 +- 0.059
82 V 0.999** 2.499 +- 0.040
89 K 0.992** 2.487 +- 0.144
129 S 1.000** 2.500 +- 0.004
198 L 0.998** 2.497 +- 0.066
206 I 0.627 1.908 +- 0.768
235 S 0.929 2.388 +- 0.404
263 V 1.000** 2.500 +- 0.015
340 S 0.858 2.275 +- 0.552
354 N 0.545 1.780 +- 0.789
355 T 0.998** 2.497 +- 0.066
356 A 0.999** 2.499 +- 0.040
419 H 0.865 2.287 +- 0.540
443 Q 1.000** 2.500 +- 0.010
447 A 0.999** 2.498 +- 0.060
458 E 0.990* 2.483 +- 0.161
