--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Feb 12 22:49:27 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_5/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_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_N2/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -30038.49 -30091.34
2 -30046.23 -30085.17
--------------------------------------
TOTAL -30039.18 -30090.65
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_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_N2/POL_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} 3.189075 0.009290 3.011557 3.386944 3.185564 1212.34 1248.47 1.000
r(A<->C){all} 0.074695 0.000015 0.067392 0.082392 0.074649 481.89 577.30 1.002
r(A<->G){all} 0.338452 0.000174 0.313705 0.364841 0.338507 357.92 391.29 1.001
r(A<->T){all} 0.032293 0.000006 0.027730 0.037102 0.032160 633.70 721.35 1.001
r(C<->G){all} 0.033943 0.000014 0.026340 0.040936 0.033830 590.08 685.87 1.000
r(C<->T){all} 0.485622 0.000208 0.455758 0.511951 0.485944 403.62 407.79 1.000
r(G<->T){all} 0.034994 0.000011 0.028866 0.041984 0.034890 558.76 597.87 1.000
pi(A){all} 0.409532 0.000051 0.396073 0.423361 0.409460 497.21 530.81 1.000
pi(C){all} 0.170107 0.000033 0.159062 0.181565 0.170054 391.93 448.86 1.000
pi(G){all} 0.209165 0.000034 0.197256 0.219914 0.209206 545.95 566.98 1.000
pi(T){all} 0.211195 0.000036 0.199195 0.222486 0.210963 569.08 611.40 1.000
alpha{1,2} 0.306852 0.000278 0.276167 0.342160 0.305701 897.35 978.45 1.001
alpha{3} 2.515981 0.064464 2.027365 2.989511 2.498368 1176.14 1194.64 1.000
pinvar{all} 0.284499 0.000315 0.250552 0.318349 0.284653 907.58 1043.34 1.001
------------------------------------------------------------------------------------------------------
* 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 -29472.106147
Model 2: PositiveSelection -29397.898141
Model 0: one-ratio -30873.153812
Model 3: discrete -29263.38663
Model 7: beta -29309.268156
Model 8: beta&w>1 -29205.096093
Model 0 vs 1 2802.0953300000037
Model 2 vs 1 148.41601199999423
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 0206.BF.x.LA13BF17.KU168268_)
Pr(w>1) post mean +- SE for w
16 P 0.958* 2.779
20 A 0.907 2.684
33 R 0.575 2.069
40 A 0.975* 2.812
41 L 0.995** 2.849
42 S 0.993** 2.845
43 F 0.881 2.636
106 L 1.000** 2.858
264 D 0.999** 2.856
303 S 0.998** 2.854
352 K 1.000** 2.857
386 Q 1.000** 2.857
427 A 0.710 2.319
475 Q 0.921 2.710
498 M 0.872 2.620
517 A 0.839 2.558
593 Q 0.825 2.533
609 S 0.964* 2.790
624 N 1.000** 2.857
695 T 1.000** 2.858
820 S 0.684 2.271
825 A 0.648 2.205
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: 0206.BF.x.LA13BF17.KU168268_)
Pr(w>1) post mean +- SE for w
16 P 0.969* 2.464 +- 0.280
20 A 0.940 2.419 +- 0.372
33 R 0.734 2.106 +- 0.670
40 A 0.986* 2.489 +- 0.203
41 L 0.996** 2.504 +- 0.140
42 S 0.996** 2.504 +- 0.142
43 F 0.918 2.386 +- 0.425
106 L 1.000** 2.510 +- 0.101
264 D 0.999** 2.509 +- 0.111
303 S 0.999** 2.508 +- 0.115
352 K 1.000** 2.510 +- 0.104
386 Q 1.000** 2.510 +- 0.105
427 A 0.833 2.256 +- 0.568
475 Q 0.955* 2.442 +- 0.326
498 M 0.953* 2.437 +- 0.328
517 A 0.902 2.362 +- 0.458
518 Q 0.679 2.019 +- 0.701
576 V 0.678 2.018 +- 0.702
593 Q 0.907 2.368 +- 0.448
609 S 0.969* 2.464 +- 0.279
624 N 1.000** 2.510 +- 0.104
695 T 1.000** 2.510 +- 0.101
820 S 0.836 2.260 +- 0.563
825 A 0.826 2.243 +- 0.575
Model 8 vs 7 208.34412599999632
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 0206.BF.x.LA13BF17.KU168268_)
Pr(w>1) post mean +- SE for w
16 P 0.997** 2.271
20 A 0.993** 2.265
33 R 0.934 2.171
40 A 0.999** 2.275
41 L 1.000** 2.276
42 S 1.000** 2.276
43 F 0.986* 2.253
106 L 1.000** 2.276
264 D 1.000** 2.276
276 T 0.537 1.544
303 S 1.000** 2.276
348 E 0.582 1.615
352 K 1.000** 2.276
386 Q 1.000** 2.276
427 A 0.973* 2.234
475 Q 0.995** 2.269
498 M 0.998** 2.273
517 A 0.987* 2.255
518 Q 0.974* 2.235
576 V 0.976* 2.237
593 Q 0.989* 2.259
609 S 0.996** 2.269
624 N 1.000** 2.276
695 T 1.000** 2.276
820 S 0.978* 2.241
825 A 0.980* 2.245
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: 0206.BF.x.LA13BF17.KU168268_)
Pr(w>1) post mean +- SE for w
16 P 0.992** 2.487 +- 0.143
20 A 0.983* 2.473 +- 0.208
33 R 0.888 2.319 +- 0.511
40 A 0.996** 2.493 +- 0.105
41 L 0.999** 2.498 +- 0.051
42 S 0.999** 2.498 +- 0.059
43 F 0.974* 2.459 +- 0.254
106 L 1.000** 2.500 +- 0.001
264 D 1.000** 2.500 +- 0.024
303 S 1.000** 2.499 +- 0.030
352 K 1.000** 2.500 +- 0.012
386 Q 1.000** 2.500 +- 0.014
427 A 0.938 2.401 +- 0.386
475 Q 0.982* 2.471 +- 0.213
498 M 0.977* 2.464 +- 0.236
517 A 0.969* 2.450 +- 0.278
518 Q 0.768 2.133 +- 0.668
576 V 0.772 2.139 +- 0.664
593 Q 0.960* 2.437 +- 0.310
609 S 0.993** 2.489 +- 0.135
624 N 1.000** 2.500 +- 0.012
695 T 1.000** 2.500 +- 0.001
820 S 0.930 2.388 +- 0.409
825 A 0.925 2.380 +- 0.421
