--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Mar 21 03:45:36 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=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS1/HIV1_AMINO/POL_1_1/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/HIV1_AMINO/POL_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/POL_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/ADOPS1/HIV1_AMINO/POL_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -31431.52 -31471.97
2 -31431.59 -31469.36
--------------------------------------
TOTAL -31431.56 -31471.35
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/HIV1_AMINO/POL_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/POL_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/ADOPS1/HIV1_AMINO/POL_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} 4.510070 0.022629 4.230193 4.811342 4.505357 679.88 743.28 1.001
r(A<->C){all} 0.078455 0.000016 0.070967 0.086601 0.078325 554.47 683.13 1.000
r(A<->G){all} 0.348014 0.000167 0.322409 0.374316 0.348070 234.84 258.73 1.000
r(A<->T){all} 0.036721 0.000007 0.031414 0.041516 0.036650 483.78 602.32 1.000
r(C<->G){all} 0.045087 0.000019 0.036157 0.053430 0.044949 612.05 639.22 1.000
r(C<->T){all} 0.456270 0.000200 0.430021 0.485619 0.455907 234.55 237.26 1.000
r(G<->T){all} 0.035452 0.000011 0.029617 0.042567 0.035410 703.04 726.53 1.000
pi(A){all} 0.416338 0.000046 0.402803 0.428972 0.416341 506.33 557.69 1.000
pi(C){all} 0.167625 0.000024 0.158655 0.177456 0.167657 510.95 563.63 1.000
pi(G){all} 0.209639 0.000031 0.198443 0.220190 0.209539 465.31 512.08 1.000
pi(T){all} 0.206398 0.000035 0.195241 0.218300 0.206358 385.75 429.03 1.000
alpha{1,2} 0.272265 0.000162 0.247468 0.296094 0.271569 943.05 1020.40 1.000
alpha{3} 1.999993 0.030385 1.675038 2.344537 1.990235 953.92 1179.25 1.000
pinvar{all} 0.228157 0.000275 0.196360 0.259934 0.228256 974.98 1038.97 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 -30815.998943
Model 2: PositiveSelection -30697.904632
Model 0: one-ratio -32431.246887
Model 3: discrete -30500.31083
Model 7: beta -30571.29679
Model 8: beta&w>1 -30437.996252
Model 0 vs 1 3230.495888000005
Model 2 vs 1 236.1886219999942
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.CN.05.FJ053.DQ859179_)
Pr(w>1) post mean +- SE for w
16 S 0.934 3.301
20 N 0.965* 3.377
31 G 0.936 3.305
32 L 1.000** 3.463
37 A 0.981* 3.416
40 F 0.593 2.460
41 S 0.996** 3.454
52 L 0.660 2.625
105 L 1.000** 3.463
264 S 0.999** 3.460
303 S 0.994** 3.448
352 S 0.993** 3.446
386 V 1.000** 3.463
427 A 1.000** 3.462
475 Q 1.000** 3.463
517 A 0.976* 3.405
609 S 0.999** 3.462
624 H 1.000** 3.463
695 S 1.000** 3.463
802 L 0.905 3.230
820 S 0.988* 3.434
825 A 0.972* 3.395
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.CN.05.FJ053.DQ859179_)
Pr(w>1) post mean +- SE for w
16 S 0.963* 3.408 +- 0.471
20 N 0.981* 3.452 +- 0.342
31 G 0.964* 3.411 +- 0.463
32 L 1.000** 3.500 +- 0.015
37 A 0.990* 3.474 +- 0.254
40 F 0.722 2.806 +- 1.119
41 S 0.998** 3.495 +- 0.114
52 L 0.782 2.956 +- 1.032
105 L 1.000** 3.500 +- 0.010
264 S 0.999** 3.498 +- 0.067
303 S 0.996** 3.491 +- 0.148
352 S 0.996** 3.491 +- 0.154
386 V 1.000** 3.500 +- 0.010
427 A 1.000** 3.499 +- 0.038
475 Q 1.000** 3.500 +- 0.013
517 A 0.987* 3.468 +- 0.282
609 S 1.000** 3.499 +- 0.044
624 H 1.000** 3.500 +- 0.012
695 S 1.000** 3.500 +- 0.029
802 L 0.946 3.366 +- 0.564
820 S 0.994** 3.484 +- 0.200
825 A 0.985* 3.461 +- 0.308
Model 8 vs 7 266.601075999999
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.CN.05.FJ053.DQ859179_)
Pr(w>1) post mean +- SE for w
11 K 0.729 1.984
16 S 0.996** 2.452
20 N 0.998** 2.456
31 G 0.993** 2.449
32 L 1.000** 2.460
37 A 0.999** 2.459
40 F 0.967* 2.401
41 S 1.000** 2.460
42 F 0.774 2.061
52 L 0.913 2.306
79 D 0.915 2.311
105 L 1.000** 2.460
264 S 1.000** 2.460
303 S 1.000** 2.460
314 L 0.677 1.893
352 S 1.000** 2.460
386 V 1.000** 2.460
418 K 0.924 2.327
427 A 1.000** 2.460
475 Q 1.000** 2.460
498 K 0.794 2.099
517 A 0.998** 2.457
609 S 1.000** 2.460
624 H 1.000** 2.460
632 S 0.547 1.663
665 E 0.664 1.867
695 S 1.000** 2.460
775 L 0.585 1.720
802 L 0.993** 2.448
820 S 0.999** 2.459
825 A 0.999** 2.458
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.CN.05.FJ053.DQ859179_)
Pr(w>1) post mean +- SE for w
11 K 0.584 1.830 +- 0.796
16 S 0.987* 2.480 +- 0.180
20 N 0.993** 2.489 +- 0.135
31 G 0.984* 2.475 +- 0.199
32 L 1.000** 2.500 +- 0.015
37 A 0.996** 2.494 +- 0.103
40 F 0.926 2.382 +- 0.419
41 S 0.999** 2.499 +- 0.050
42 F 0.729 2.058 +- 0.728
52 L 0.891 2.322 +- 0.510
79 D 0.707 2.036 +- 0.723
105 L 1.000** 2.500 +- 0.011
264 S 0.999** 2.499 +- 0.037
303 S 0.999** 2.498 +- 0.059
352 S 0.998** 2.498 +- 0.064
386 V 1.000** 2.500 +- 0.011
418 K 0.855 2.267 +- 0.566
427 A 1.000** 2.500 +- 0.025
475 Q 1.000** 2.500 +- 0.013
498 K 0.518 1.733 +- 0.797
517 A 0.995** 2.492 +- 0.115
609 S 1.000** 2.500 +- 0.030
624 H 1.000** 2.500 +- 0.013
665 E 0.574 1.809 +- 0.806
695 S 1.000** 2.500 +- 0.019
775 L 0.607 1.842 +- 0.823
802 L 0.980* 2.468 +- 0.223
820 S 0.997** 2.495 +- 0.089
825 A 0.995** 2.492 +- 0.113
