--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Feb 12 06:04:32 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_N2/POL_1_4/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_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_N2/POL_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -32200.00 -32240.54
2 -32197.19 -32237.04
--------------------------------------
TOTAL -32197.82 -32239.88
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_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_N2/POL_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} 4.528076 0.022500 4.238315 4.825170 4.521645 514.52 782.28 1.000
r(A<->C){all} 0.080871 0.000015 0.073167 0.088600 0.080777 794.03 809.91 1.000
r(A<->G){all} 0.346356 0.000178 0.317368 0.371422 0.346772 289.45 307.69 1.000
r(A<->T){all} 0.034837 0.000006 0.030259 0.039725 0.034722 616.54 680.57 1.000
r(C<->G){all} 0.036741 0.000016 0.029067 0.044800 0.036634 511.65 592.14 1.001
r(C<->T){all} 0.464710 0.000202 0.435600 0.491353 0.464635 255.63 275.82 1.000
r(G<->T){all} 0.036485 0.000011 0.030119 0.042840 0.036431 824.78 828.67 1.000
pi(A){all} 0.419994 0.000049 0.406275 0.433531 0.419819 440.95 517.53 1.000
pi(C){all} 0.168446 0.000028 0.157954 0.178537 0.168374 446.19 449.13 1.000
pi(G){all} 0.204878 0.000028 0.194317 0.214761 0.204916 498.39 563.89 1.000
pi(T){all} 0.206683 0.000034 0.196076 0.218470 0.206542 430.76 492.63 1.000
alpha{1,2} 0.267239 0.000161 0.240936 0.290561 0.267113 1097.08 1144.55 1.000
alpha{3} 2.485673 0.051842 2.070056 2.943386 2.472733 1256.15 1288.56 1.000
pinvar{all} 0.232979 0.000262 0.201076 0.264822 0.233068 627.89 869.74 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 -31020.236433
Model 2: PositiveSelection -30867.336546
Model 0: one-ratio -32712.450941
Model 3: discrete -30685.050346
Model 7: beta -30804.215158
Model 8: beta&w>1 -30631.594021
Model 0 vs 1 3384.429016000002
Model 2 vs 1 305.79977399999916
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: B.US.11.AMBI_CLONE.KU641402_)
Pr(w>1) post mean +- SE for w
17 P 1.000** 4.215
32 T 1.000** 4.215
33 F 0.998** 4.210
98 S 1.000** 4.215
344 R 0.999** 4.212
378 V 1.000** 4.215
419 A 0.994** 4.194
467 Q 1.000** 4.215
509 A 0.994** 4.196
601 S 1.000** 4.215
616 H 0.998** 4.210
687 T 1.000** 4.215
812 S 1.000** 4.215
817 T 1.000** 4.215
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: B.US.11.AMBI_CLONE.KU641402_)
Pr(w>1) post mean +- SE for w
17 P 1.000** 3.685 +- 0.389
32 T 1.000** 3.685 +- 0.389
33 F 0.999** 3.684 +- 0.393
98 S 1.000** 3.685 +- 0.389
256 D 0.695 2.797 +- 1.212
344 R 1.000** 3.684 +- 0.391
378 V 1.000** 3.685 +- 0.389
419 A 0.998** 3.679 +- 0.408
467 Q 1.000** 3.685 +- 0.389
490 V 0.649 2.637 +- 1.210
509 A 0.998** 3.679 +- 0.407
510 T 0.721 2.827 +- 1.145
601 S 1.000** 3.685 +- 0.389
616 H 1.000** 3.684 +- 0.393
624 L 0.661 2.688 +- 1.224
687 T 1.000** 3.685 +- 0.389
812 S 1.000** 3.685 +- 0.389
817 T 1.000** 3.685 +- 0.389
Model 8 vs 7 345.24227399999654
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: B.US.11.AMBI_CLONE.KU641402_)
Pr(w>1) post mean +- SE for w
17 P 1.000** 2.643
30 Q 0.746 2.143
32 T 1.000** 2.643
33 F 1.000** 2.643
35 F 0.619 1.890
72 S 0.875 2.397
98 S 1.000** 2.643
256 D 0.990** 2.624
344 R 1.000** 2.643
378 V 1.000** 2.643
419 A 1.000** 2.643
467 Q 1.000** 2.643
490 V 0.999** 2.641
509 A 1.000** 2.643
510 T 0.999** 2.642
568 V 0.987* 2.618
585 L 0.953* 2.551
601 S 1.000** 2.643
616 H 1.000** 2.643
624 L 0.993** 2.629
687 T 1.000** 2.643
765 V 0.957* 2.558
767 L 0.803 2.254
812 S 1.000** 2.643
817 T 1.000** 2.643
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: B.US.11.AMBI_CLONE.KU641402_)
Pr(w>1) post mean +- SE for w
17 P 1.000** 2.524 +- 0.152
21 A 0.537 1.735 +- 0.833
30 Q 0.745 2.088 +- 0.717
32 T 1.000** 2.524 +- 0.152
33 F 1.000** 2.523 +- 0.153
35 F 0.689 1.991 +- 0.774
72 S 0.744 2.093 +- 0.697
98 S 1.000** 2.524 +- 0.152
256 D 0.972* 2.474 +- 0.300
344 R 1.000** 2.524 +- 0.152
378 V 1.000** 2.524 +- 0.152
419 A 0.999** 2.523 +- 0.156
467 Q 1.000** 2.524 +- 0.152
490 V 0.980* 2.484 +- 0.252
509 A 0.999** 2.523 +- 0.156
510 T 0.986* 2.495 +- 0.226
568 V 0.918 2.374 +- 0.439
585 L 0.899 2.347 +- 0.494
601 S 1.000** 2.524 +- 0.152
616 H 1.000** 2.523 +- 0.153
624 L 0.973* 2.474 +- 0.293
687 T 1.000** 2.524 +- 0.152
765 V 0.918 2.380 +- 0.457
767 L 0.842 2.251 +- 0.626
794 L 0.520 1.705 +- 0.840
812 S 1.000** 2.524 +- 0.152
817 T 1.000** 2.524 +- 0.152
