--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Mar 23 17:31:00 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_4/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/HIV1_AMINO/POL_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/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/ADOPS1/HIV1_AMINO/POL_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -32019.53 -32063.92
2 -32023.26 -32067.52
--------------------------------------
TOTAL -32020.20 -32066.85
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/HIV1_AMINO/POL_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/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/ADOPS1/HIV1_AMINO/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} 4.441065 0.023222 4.150289 4.732285 4.441427 477.91 565.90 1.000
r(A<->C){all} 0.082099 0.000016 0.074269 0.089541 0.081973 635.31 652.45 1.000
r(A<->G){all} 0.343648 0.000159 0.316881 0.366342 0.343305 258.72 295.90 1.001
r(A<->T){all} 0.035443 0.000006 0.030560 0.040157 0.035412 664.52 758.42 1.000
r(C<->G){all} 0.040414 0.000016 0.032540 0.048144 0.040304 703.56 725.35 1.002
r(C<->T){all} 0.455836 0.000183 0.429183 0.482523 0.456097 245.32 303.50 1.000
r(G<->T){all} 0.042559 0.000013 0.035681 0.049546 0.042434 654.76 739.14 1.000
pi(A){all} 0.413391 0.000048 0.400124 0.427163 0.413283 380.19 505.75 1.000
pi(C){all} 0.169779 0.000026 0.159917 0.179514 0.169876 413.74 434.70 1.001
pi(G){all} 0.208506 0.000030 0.197701 0.219167 0.208434 407.40 507.69 1.000
pi(T){all} 0.208325 0.000034 0.196599 0.219976 0.208098 477.72 527.70 1.000
alpha{1,2} 0.271833 0.000190 0.244307 0.298083 0.271162 902.63 1037.12 1.000
alpha{3} 1.846141 0.028457 1.549817 2.206889 1.835793 1035.94 1073.92 1.000
pinvar{all} 0.233658 0.000299 0.200053 0.265875 0.233762 690.49 780.28 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 -31440.889907
Model 2: PositiveSelection -31361.228449
Model 0: one-ratio -32961.858322
Model 3: discrete -31127.923568
Model 7: beta -31177.634244
Model 8: beta&w>1 -31070.761562
Model 0 vs 1 3041.9368299999987
Model 2 vs 1 159.32291600000462
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.ZM.05.ZM410F.KM050667_)
Pr(w>1) post mean +- SE for w
21 T 0.646 2.277
32 Q 0.878 2.736
40 L 0.540 2.069
105 P 1.000** 2.977
264 N 1.000** 2.977
352 K 0.962* 2.903
386 V 1.000** 2.977
427 A 0.965* 2.909
475 H 0.540 2.069
498 T 0.994** 2.965
517 A 0.973* 2.924
576 V 0.872 2.724
593 I 0.843 2.667
609 S 0.956* 2.891
624 Q 0.984* 2.947
695 S 1.000** 2.977
773 I 0.556 2.099
825 A 1.000** 2.977
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: C.ZM.05.ZM410F.KM050667_)
Pr(w>1) post mean +- SE for w
17 P 0.686 2.039 +- 0.710
21 T 0.827 2.257 +- 0.588
32 Q 0.934 2.424 +- 0.406
35 S 0.506 1.763 +- 0.757
40 L 0.790 2.197 +- 0.627
41 N 0.643 1.968 +- 0.724
52 L 0.510 1.773 +- 0.763
105 P 1.000** 2.525 +- 0.155
264 N 1.000** 2.525 +- 0.155
348 E 0.568 1.855 +- 0.749
352 K 0.984* 2.499 +- 0.245
386 V 1.000** 2.525 +- 0.155
427 A 0.978* 2.492 +- 0.269
475 H 0.811 2.228 +- 0.602
498 T 0.998** 2.521 +- 0.170
517 A 0.983* 2.499 +- 0.249
518 M 0.782 2.176 +- 0.623
576 V 0.967* 2.469 +- 0.304
593 I 0.938 2.427 +- 0.394
609 S 0.971* 2.480 +- 0.299
624 Q 0.992** 2.512 +- 0.208
632 S 0.600 1.903 +- 0.739
695 S 1.000** 2.525 +- 0.155
773 I 0.810 2.228 +- 0.604
775 I 0.533 1.808 +- 0.762
802 I 0.723 2.096 +- 0.686
820 T 0.551 1.829 +- 0.750
825 A 1.000** 2.524 +- 0.157
Model 8 vs 7 213.74536400000216
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.ZM.05.ZM410F.KM050667_)
Pr(w>1) post mean +- SE for w
17 P 0.941 2.036
21 T 0.980* 2.094
27 T 0.787 1.809
32 Q 0.993** 2.113
35 S 0.877 1.942
40 L 0.977* 2.089
41 N 0.963* 2.068
42 C 0.597 1.528
52 L 0.802 1.831
105 P 1.000** 2.123
264 N 1.000** 2.123
303 S 0.569 1.492
348 E 0.948 2.047
352 K 0.999** 2.122
386 V 1.000** 2.123
418 R 0.820 1.859
427 A 0.999** 2.121
475 H 0.982* 2.096
498 T 1.000** 2.123
517 A 0.999** 2.121
518 M 0.994** 2.115
576 V 1.000** 2.122
593 I 0.997** 2.118
609 S 0.997** 2.119
624 Q 1.000** 2.122
632 S 0.954* 2.055
695 S 1.000** 2.123
773 I 0.985* 2.101
775 I 0.806 1.837
802 I 0.965* 2.071
820 T 0.937 2.030
825 A 1.000** 2.123
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: C.ZM.05.ZM410F.KM050667_)
Pr(w>1) post mean +- SE for w
17 P 0.830 2.224 +- 0.610
21 T 0.926 2.382 +- 0.421
27 T 0.600 1.842 +- 0.809
32 Q 0.974* 2.459 +- 0.254
35 S 0.669 1.962 +- 0.768
40 L 0.885 2.315 +- 0.513
41 N 0.726 2.061 +- 0.715
52 L 0.664 1.946 +- 0.781
105 P 1.000** 2.500 +- 0.001
264 N 1.000** 2.500 +- 0.001
348 E 0.659 1.954 +- 0.760
352 K 0.993** 2.488 +- 0.135
386 V 1.000** 2.500 +- 0.001
427 A 0.994** 2.490 +- 0.124
475 H 0.869 2.290 +- 0.540
498 T 0.999** 2.498 +- 0.060
517 A 0.995** 2.492 +- 0.111
518 M 0.787 2.163 +- 0.647
576 V 0.979* 2.467 +- 0.227
593 I 0.969* 2.451 +- 0.275
609 S 0.991** 2.486 +- 0.150
624 Q 0.996** 2.494 +- 0.094
632 S 0.685 1.995 +- 0.745
695 S 1.000** 2.500 +- 0.001
773 I 0.895 2.332 +- 0.490
775 I 0.706 2.013 +- 0.758
802 I 0.847 2.255 +- 0.579
820 T 0.651 1.940 +- 0.767
825 A 1.000** 2.500 +- 0.014
