--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Feb 10 03:36:34 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_1/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/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/ADOPS/HIV1_N2/POL_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -29294.16 -29335.91
2 -29290.05 -29330.12
--------------------------------------
TOTAL -29290.73 -29335.22
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/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/ADOPS/HIV1_N2/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} 3.025380 0.007731 2.849271 3.191844 3.024690 1211.82 1315.97 1.000
r(A<->C){all} 0.077046 0.000016 0.069749 0.084951 0.077051 698.39 706.38 1.000
r(A<->G){all} 0.372788 0.000185 0.345021 0.398314 0.372560 332.90 383.68 1.002
r(A<->T){all} 0.038019 0.000007 0.033240 0.043029 0.037954 664.41 704.96 1.000
r(C<->G){all} 0.029808 0.000013 0.023045 0.037032 0.029563 805.87 871.35 1.000
r(C<->T){all} 0.443925 0.000205 0.414947 0.469977 0.444149 327.31 362.21 1.002
r(G<->T){all} 0.038414 0.000012 0.031867 0.045197 0.038370 799.50 808.66 1.002
pi(A){all} 0.405195 0.000052 0.390890 0.418645 0.405402 671.93 683.87 1.000
pi(C){all} 0.178187 0.000031 0.167600 0.189189 0.178153 582.61 582.62 1.000
pi(G){all} 0.206618 0.000035 0.194570 0.218007 0.206711 592.97 691.75 1.002
pi(T){all} 0.210000 0.000037 0.198688 0.222128 0.210029 556.26 583.72 1.001
alpha{1,2} 0.267008 0.000223 0.238769 0.296443 0.266618 1155.38 1297.75 1.000
alpha{3} 2.327650 0.066804 1.810664 2.801887 2.316513 975.66 1202.89 1.002
pinvar{all} 0.265641 0.000352 0.230841 0.303320 0.265794 1030.77 1154.94 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 -28722.613283
Model 2: PositiveSelection -28636.150282
Model 0: one-ratio -30080.551681
Model 3: discrete -28515.40265
Model 7: beta -28566.048946
Model 8: beta&w>1 -28460.402236
Model 0 vs 1 2715.876796000004
Model 2 vs 1 172.92600200000015
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.TH.05.AA029b10L.JX447033_)
Pr(w>1) post mean +- SE for w
16 S 0.980* 3.311
30 G 0.998** 3.354
42 F 0.899 3.120
44 F 0.669 2.578
107 L 1.000** 3.359
266 S 1.000** 3.359
350 A 0.943 3.225
354 S 0.999** 3.357
388 E 1.000** 3.359
429 A 0.988* 3.331
477 Q 1.000** 3.358
519 A 0.996** 3.349
595 L 0.958* 3.259
611 S 0.992** 3.340
626 H 1.000** 3.358
697 S 1.000** 3.359
720 S 0.504 2.189
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.TH.05.AA029b10L.JX447033_)
Pr(w>1) post mean +- SE for w
16 S 0.990* 3.454 +- 0.286
30 G 0.999** 3.477 +- 0.164
41 S 0.549 2.359 +- 1.237
42 F 0.942 3.334 +- 0.598
44 F 0.790 2.957 +- 1.018
107 L 1.000** 3.479 +- 0.144
266 S 1.000** 3.479 +- 0.145
350 A 0.967* 3.398 +- 0.463
354 S 1.000** 3.478 +- 0.151
388 E 1.000** 3.479 +- 0.144
429 A 0.994** 3.464 +- 0.238
477 Q 1.000** 3.479 +- 0.148
519 A 0.998** 3.474 +- 0.184
595 L 0.977* 3.421 +- 0.401
611 S 0.996** 3.470 +- 0.210
626 H 1.000** 3.478 +- 0.149
697 S 1.000** 3.479 +- 0.144
720 S 0.607 2.499 +- 1.213
804 L 0.595 2.473 +- 1.221
Model 8 vs 7 211.2934199999945
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.TH.05.AA029b10L.JX447033_)
Pr(w>1) post mean +- SE for w
11 K 0.863 2.215
16 S 0.998** 2.447
21 A 0.822 2.143
30 G 1.000** 2.450
41 S 0.834 2.161
42 F 0.993** 2.438
44 F 0.949 2.361
107 L 1.000** 2.450
266 S 1.000** 2.450
278 I 0.874 2.233
305 C 0.657 1.859
350 A 0.998** 2.446
354 S 1.000** 2.450
358 T 0.802 2.107
388 E 1.000** 2.450
429 A 0.999** 2.449
477 Q 1.000** 2.450
519 A 1.000** 2.450
595 L 0.998** 2.446
611 S 0.999** 2.449
626 H 1.000** 2.450
634 S 0.941 2.349
697 S 1.000** 2.450
720 S 0.978* 2.412
775 V 0.916 2.305
804 L 0.870 2.225
827 A 0.777 2.066
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.TH.05.AA029b10L.JX447033_)
Pr(w>1) post mean +- SE for w
11 K 0.793 2.169 +- 0.650
16 S 0.996** 2.494 +- 0.098
21 A 0.815 2.200 +- 0.633
30 G 0.999** 2.499 +- 0.040
41 S 0.850 2.254 +- 0.587
42 F 0.986* 2.478 +- 0.186
44 F 0.941 2.405 +- 0.381
107 L 1.000** 2.500 +- 0.004
266 S 1.000** 2.500 +- 0.011
278 I 0.677 1.989 +- 0.741
305 C 0.552 1.780 +- 0.800
350 A 0.992** 2.487 +- 0.143
354 S 1.000** 2.500 +- 0.020
358 T 0.782 2.147 +- 0.671
388 E 1.000** 2.500 +- 0.004
429 A 0.998** 2.497 +- 0.071
477 Q 1.000** 2.500 +- 0.018
519 A 0.999** 2.499 +- 0.047
595 L 0.994** 2.490 +- 0.127
611 S 0.998** 2.497 +- 0.069
626 H 1.000** 2.500 +- 0.019
634 S 0.899 2.338 +- 0.483
697 S 1.000** 2.500 +- 0.005
720 S 0.948 2.418 +- 0.352
775 V 0.864 2.283 +- 0.548
804 L 0.860 2.273 +- 0.564
827 A 0.688 2.000 +- 0.744
