--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Feb 10 23:10:08 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_2/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -30003.54 -30045.47
2 -30005.35 -30046.08
--------------------------------------
TOTAL -30004.08 -30045.82
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 3.120844 0.007473 2.950945 3.289556 3.118392 1167.33 1206.02 1.000
r(A<->C){all} 0.077608 0.000016 0.069511 0.085079 0.077500 657.56 717.87 1.000
r(A<->G){all} 0.345174 0.000152 0.321095 0.368907 0.345328 309.57 401.82 1.002
r(A<->T){all} 0.033282 0.000005 0.028743 0.037685 0.033200 593.55 786.45 1.000
r(C<->G){all} 0.040371 0.000017 0.032272 0.048584 0.040184 698.10 732.12 1.001
r(C<->T){all} 0.462310 0.000178 0.436367 0.488444 0.462479 363.85 441.23 1.001
r(G<->T){all} 0.041256 0.000013 0.035061 0.048820 0.041127 730.29 803.33 1.000
pi(A){all} 0.410060 0.000050 0.395844 0.422988 0.410183 791.09 867.55 1.000
pi(C){all} 0.169847 0.000030 0.158516 0.180136 0.169835 603.97 626.13 1.002
pi(G){all} 0.203739 0.000029 0.193303 0.214697 0.203627 608.08 715.16 1.000
pi(T){all} 0.216353 0.000036 0.204959 0.228330 0.216299 762.62 798.84 1.000
alpha{1,2} 0.289572 0.000206 0.263101 0.318406 0.288809 889.74 994.56 1.000
alpha{3} 2.404885 0.060077 1.939702 2.864435 2.387794 1179.84 1245.41 1.000
pinvar{all} 0.266603 0.000297 0.233151 0.299325 0.266780 940.60 1053.83 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 -29370.480694
Model 2: PositiveSelection -29291.241634
Model 0: one-ratio -30818.626155
Model 3: discrete -29164.468606
Model 7: beta -29225.191414
Model 8: beta&w>1 -29118.940595
Model 0 vs 1 2896.290922
Model 2 vs 1 158.47811999999976
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.00.ES1_20.EF363123_)
Pr(w>1) post mean +- SE for w
17 S 0.919 2.792
33 S 0.993** 2.937
34 L 1.000** 2.951
41 T 0.953* 2.859
42 L 0.985* 2.923
43 S 0.960* 2.874
54 L 0.851 2.661
107 P 1.000** 2.951
266 E 1.000** 2.951
278 T 0.719 2.403
305 S 0.865 2.688
350 Q 0.591 2.153
354 K 0.988* 2.927
388 V 0.767 2.497
429 T 0.614 2.198
519 T 0.542 2.057
611 S 0.947 2.847
626 H 1.000** 2.951
697 A 1.000** 2.951
775 I 0.902 2.761
804 I 0.978* 2.909
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.00.ES1_20.EF363123_)
Pr(w>1) post mean +- SE for w
17 S 0.949 2.441 +- 0.360
21 T 0.544 1.821 +- 0.755
32 R 0.825 2.241 +- 0.573
33 S 0.992** 2.507 +- 0.191
34 L 1.000** 2.519 +- 0.137
41 T 0.978* 2.486 +- 0.258
42 L 0.990** 2.504 +- 0.203
43 S 0.981* 2.490 +- 0.248
54 L 0.908 2.379 +- 0.458
107 P 1.000** 2.519 +- 0.137
266 E 1.000** 2.519 +- 0.137
278 T 0.921 2.390 +- 0.418
305 S 0.952* 2.442 +- 0.347
350 Q 0.825 2.246 +- 0.582
354 K 0.993** 2.508 +- 0.186
388 V 0.894 2.355 +- 0.482
429 T 0.796 2.205 +- 0.619
503 A 0.686 2.036 +- 0.706
519 T 0.742 2.123 +- 0.670
611 S 0.960* 2.459 +- 0.325
626 H 1.000** 2.519 +- 0.137
660 L 0.580 1.873 +- 0.745
697 A 1.000** 2.519 +- 0.137
775 I 0.952* 2.445 +- 0.351
804 I 0.985* 2.496 +- 0.229
826 T 0.726 2.094 +- 0.675
Model 8 vs 7 212.50163800000155
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.00.ES1_20.EF363123_)
Pr(w>1) post mean +- SE for w
5 N 0.945 1.963
12 K 0.678 1.594
16 L 0.688 1.607
17 S 0.996** 2.033
21 T 0.912 1.917
32 R 0.998** 2.036
33 S 0.999** 2.038
34 L 1.000** 2.039
41 T 0.999** 2.038
42 L 1.000** 2.038
43 S 0.999** 2.038
44 F 0.783 1.736
54 L 0.988* 2.023
81 N 0.853 1.836
107 P 1.000** 2.039
137 I 0.523 1.378
266 E 1.000** 2.039
278 T 0.999** 2.038
305 S 0.999** 2.037
350 Q 0.993** 2.029
354 K 1.000** 2.038
357 F 0.631 1.527
388 V 0.995** 2.032
420 R 0.906 1.910
429 T 0.981* 2.012
477 Q 0.886 1.881
503 A 0.965* 1.990
519 T 0.969* 1.995
520 T 0.948 1.967
578 V 0.930 1.942
595 S 0.915 1.921
611 S 0.996** 2.034
626 H 1.000** 2.039
660 L 0.952* 1.973
674 I 0.508 1.353
697 A 1.000** 2.039
731 L 0.543 1.390
775 I 0.998** 2.036
777 L 0.755 1.695
804 I 0.999** 2.038
826 T 0.985* 2.018
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.00.ES1_20.EF363123_)
Pr(w>1) post mean +- SE for w
17 S 0.985* 2.476 +- 0.196
21 T 0.740 2.077 +- 0.717
32 R 0.866 2.288 +- 0.538
33 S 0.998** 2.497 +- 0.063
34 L 1.000** 2.500 +- 0.001
41 T 0.991** 2.486 +- 0.146
42 L 0.997** 2.495 +- 0.088
43 S 0.993** 2.488 +- 0.135
44 F 0.574 1.796 +- 0.823
54 L 0.965* 2.444 +- 0.295
107 P 1.000** 2.500 +- 0.002
266 E 1.000** 2.500 +- 0.001
278 T 0.947 2.417 +- 0.351
305 S 0.977* 2.464 +- 0.237
350 Q 0.897 2.337 +- 0.482
354 K 0.998** 2.496 +- 0.075
388 V 0.953* 2.425 +- 0.337
429 T 0.915 2.364 +- 0.448
503 A 0.843 2.247 +- 0.587
519 T 0.887 2.318 +- 0.512
595 S 0.523 1.733 +- 0.807
611 S 0.990* 2.483 +- 0.163
626 H 1.000** 2.500 +- 0.003
660 L 0.717 2.044 +- 0.726
697 A 1.000** 2.500 +- 0.004
775 I 0.983* 2.472 +- 0.208
777 L 0.620 1.864 +- 0.818
804 I 0.996** 2.493 +- 0.105
826 T 0.844 2.251 +- 0.580
