--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Mar 15 21:22:40 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_A1/ENV_1_2/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_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_A1/ENV_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -49253.20        -49295.51
2     -49251.92        -49291.59
--------------------------------------
TOTAL   -49252.37        -49294.83
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_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_A1/ENV_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}         8.520280    0.070648    8.006031    9.029888    8.512646    880.50    906.37    1.000
r(A<->C){all}   0.132237    0.000027    0.121210    0.141730    0.132403    346.67    409.01    1.000
r(A<->G){all}   0.299126    0.000140    0.276629    0.321858    0.299409    172.85    225.56    1.001
r(A<->T){all}   0.056602    0.000011    0.050060    0.062777    0.056502    601.82    674.36    1.000
r(C<->G){all}   0.067927    0.000023    0.058703    0.077256    0.067770    517.03    613.55    1.003
r(C<->T){all}   0.346730    0.000156    0.323732    0.371366    0.346299    206.96    215.76    1.001
r(G<->T){all}   0.097379    0.000026    0.087467    0.106972    0.097266    366.65    396.22    1.004
pi(A){all}      0.397327    0.000049    0.383806    0.410914    0.397330    410.80    426.42    1.000
pi(C){all}      0.175425    0.000028    0.164550    0.184760    0.175509    266.64    299.75    1.000
pi(G){all}      0.220099    0.000034    0.208299    0.231055    0.219879    180.26    296.49    1.000
pi(T){all}      0.207149    0.000035    0.194870    0.218344    0.207041    361.43    385.63    1.000
alpha{1,2}      0.483374    0.000519    0.442819    0.528907    0.482658   1051.31   1087.49    1.000
alpha{3}        1.056696    0.004022    0.925692    1.174112    1.056890    985.27   1052.47    1.000
pinvar{all}     0.187538    0.000204    0.160950    0.216355    0.187694   1031.23   1058.84    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	-40805.901807
Model 2: PositiveSelection	-40168.634087
Model 0: one-ratio	-43375.868154
Model 3: discrete	-40136.944168
Model 7: beta	-40606.662897
Model 8: beta&w>1	-40033.544763


Model 0 vs 1	5139.932694000003

Model 2 vs 1	1274.535440000007

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.06.98PB2.EU743784_)

            Pr(w>1)     post mean +- SE for w

    10 W      1.000**       3.483
    15 T      0.990**       3.459
    73 Y      1.000**       3.483
   119 P      1.000**       3.483
   120 T      1.000**       3.482
   121 T      1.000**       3.483
   122 S      1.000**       3.483
   139 K      0.871         3.162
   140 Q      1.000**       3.483
   143 Y      0.987*        3.451
   155 N      0.995**       3.471
   156 K      1.000**       3.483
   157 T      1.000**       3.483
   158 T      1.000**       3.483
   168 V      0.998**       3.479
   177 S      0.541         2.344
   200 N      0.546         2.357
   208 N      0.992**       3.462
   249 T      0.956*        3.373
   259 S      0.575         2.429
   261 Q      1.000**       3.483
   268 S      0.999**       3.480
   276 H      1.000**       3.483
   286 D      1.000**       3.483
   299 G      0.992**       3.463
   300 T      1.000**       3.483
   303 E      0.998**       3.479
   306 K      1.000**       3.483
   307 Q      1.000**       3.483
   309 A      1.000**       3.483
   310 K      1.000**       3.483
   313 K      1.000**       3.483
   315 H      0.780         2.938
   319 V      1.000**       3.483
   323 S      0.999**       3.481
   347 S      0.575         2.428
   348 Q      1.000**       3.483
   352 A      0.962*        3.388
   354 T      1.000**       3.483
   355 I      1.000**       3.483
   357 S      1.000**       3.483
   358 T      0.970*        3.408
   385 S      1.000**       3.483
   387 V      1.000**       3.483
   391 L      1.000**       3.483
   405 N      1.000**       3.483
   406 T      1.000**       3.483
   407 A      1.000**       3.483
   456 I      0.779         2.934
   548 A      1.000**       3.483
   553 S      0.999**       3.481
   560 Y      1.000**       3.483
   561 D      1.000**       3.483
   562 T      1.000**       3.483
   570 K      0.556         2.379
   576 S      0.691         2.717
   580 D      1.000**       3.483
   581 L      1.000**       3.483
   584 G      1.000**       3.483
   614 D      0.998**       3.479
   661 T      1.000**       3.483
   663 H      0.988*        3.453
   664 Q      0.903         3.242
   686 V      1.000**       3.483
   690 S      0.999**       3.481
   696 A      1.000**       3.482
   710 R      1.000**       3.483
   726 G      1.000**       3.483
   730 L      0.789         2.958
   735 L      0.999**       3.481
   749 L      0.546         2.356
   770 A      1.000**       3.483
   771 W      1.000**       3.483
   775 L      0.998**       3.478
   776 H      0.694         2.724
   785 L      0.990*        3.458

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.TH.06.98PB2.EU743784_)

            Pr(w>1)     post mean +- SE for w

    10 W      1.000**       3.500 +- 0.012
    15 T      0.989*        3.473 +- 0.261
    73 Y      1.000**       3.500 +- 0.000
   119 P      1.000**       3.500 +- 0.000
   120 T      1.000**       3.500 +- 0.035
   121 T      1.000**       3.500 +- 0.000
   122 S      1.000**       3.500 +- 0.000
   139 K      0.851         3.129 +- 0.889
   140 Q      1.000**       3.500 +- 0.017
   143 Y      0.985*        3.462 +- 0.304
   155 N      0.994**       3.486 +- 0.189
   156 K      1.000**       3.500 +- 0.003
   157 T      1.000**       3.500 +- 0.000
   158 T      1.000**       3.500 +- 0.001
   168 V      0.998**       3.495 +- 0.106
   177 S      0.513         2.283 +- 1.250
   200 N      0.513         2.281 +- 1.250
   208 N      0.990**       3.476 +- 0.246
   249 T      0.949         3.372 +- 0.551
   259 S      0.544         2.360 +- 1.245
   261 Q      1.000**       3.500 +- 0.000
   268 S      0.999**       3.496 +- 0.094
   276 H      1.000**       3.500 +- 0.009
   286 D      1.000**       3.500 +- 0.002
   299 G      0.990**       3.476 +- 0.243
   300 T      1.000**       3.500 +- 0.009
   303 E      0.998**       3.495 +- 0.107
   306 K      1.000**       3.500 +- 0.018
   307 Q      1.000**       3.500 +- 0.000
   309 A      1.000**       3.500 +- 0.017
   310 K      1.000**       3.500 +- 0.000
   313 K      1.000**       3.500 +- 0.007
   315 H      0.755         2.888 +- 1.075
   319 V      1.000**       3.500 +- 0.000
   323 S      0.999**       3.498 +- 0.063
   347 S      0.544         2.361 +- 1.245
   348 Q      1.000**       3.500 +- 0.000
   352 A      0.956*        3.389 +- 0.515
   354 T      1.000**       3.500 +- 0.000
   355 I      1.000**       3.500 +- 0.000
   357 S      1.000**       3.500 +- 0.000
   358 T      0.965*        3.412 +- 0.460
   385 S      1.000**       3.500 +- 0.000
   387 V      1.000**       3.500 +- 0.000
   391 L      1.000**       3.500 +- 0.012
   405 N      1.000**       3.500 +- 0.000
   406 T      1.000**       3.500 +- 0.000
   407 A      1.000**       3.500 +- 0.000
   456 I      0.754         2.885 +- 1.076
   548 A      1.000**       3.500 +- 0.024
   553 S      0.999**       3.498 +- 0.067
   560 Y      1.000**       3.500 +- 0.000
   561 D      1.000**       3.500 +- 0.001
   562 T      1.000**       3.500 +- 0.011
   570 K      0.525         2.313 +- 1.248
   576 S      0.658         2.645 +- 1.186
   580 D      1.000**       3.500 +- 0.000
   581 L      1.000**       3.500 +- 0.033
   584 G      1.000**       3.500 +- 0.000
   614 D      0.998**       3.496 +- 0.106
   661 T      1.000**       3.500 +- 0.026
   663 H      0.986*        3.465 +- 0.293
   664 Q      0.890         3.226 +- 0.781
   686 V      1.000**       3.500 +- 0.014
   690 S      0.999**       3.498 +- 0.067
   696 A      1.000**       3.499 +- 0.039
   710 R      1.000**       3.500 +- 0.005
   726 G      1.000**       3.500 +- 0.001
   730 L      0.767         2.918 +- 1.056
   735 L      0.999**       3.498 +- 0.077
   749 L      0.515         2.288 +- 1.249
   770 A      1.000**       3.500 +- 0.006
   771 W      1.000**       3.500 +- 0.007
   775 L      0.998**       3.494 +- 0.124
   776 H      0.665         2.661 +- 1.180
   785 L      0.988*        3.471 +- 0.269


Model 8 vs 7	1146.2362680000078

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.06.98PB2.EU743784_)

            Pr(w>1)     post mean +- SE for w

    10 W      1.000**       3.021
    15 T      0.990**       3.001
    73 Y      1.000**       3.021
   119 P      1.000**       3.021
   120 T      1.000**       3.021
   121 T      1.000**       3.021
   122 S      1.000**       3.021
   139 K      0.879         2.772
   140 Q      1.000**       3.021
   143 Y      0.987*        2.995
   155 N      0.994**       3.009
   156 K      1.000**       3.021
   157 T      1.000**       3.021
   158 T      1.000**       3.021
   168 V      0.998**       3.018
   177 S      0.647         2.280
   200 N      0.597         2.185
   208 N      0.991**       3.002
   249 T      0.966*        2.950
   259 S      0.669         2.332
   261 Q      1.000**       3.021
   268 S      0.998**       3.018
   276 H      1.000**       3.021
   286 D      1.000**       3.021
   299 G      0.990**       3.001
   300 T      1.000**       3.021
   303 E      0.998**       3.017
   306 K      1.000**       3.021
   307 Q      1.000**       3.021
   309 A      1.000**       3.021
   310 K      1.000**       3.021
   313 K      1.000**       3.021
   315 H      0.806         2.618
   319 V      1.000**       3.021
   323 S      0.999**       3.020
   347 S      0.689         2.371
   348 Q      1.000**       3.021
   352 A      0.956*        2.930
   354 T      1.000**       3.021
   355 I      1.000**       3.021
   357 S      1.000**       3.021
   358 T      0.972*        2.963
   385 S      1.000**       3.021
   387 V      1.000**       3.021
   391 L      1.000**       3.021
   405 N      1.000**       3.021
   406 T      1.000**       3.021
   407 A      1.000**       3.021
   442 R      0.503         1.988
   456 I      0.800         2.607
   548 A      1.000**       3.021
   553 S      0.999**       3.020
   560 Y      1.000**       3.021
   561 D      1.000**       3.021
   562 T      1.000**       3.021
   570 K      0.623         2.234
   576 S      0.730         2.462
   580 D      1.000**       3.021
   581 L      1.000**       3.021
   584 G      1.000**       3.021
   614 D      0.998**       3.017
   661 T      1.000**       3.021
   663 H      0.989*        2.999
   664 Q      0.926         2.866
   686 V      1.000**       3.021
   690 S      0.999**       3.019
   696 A      1.000**       3.021
   710 R      1.000**       3.021
   726 G      1.000**       3.021
   730 L      0.811         2.623
   735 L      0.999**       3.019
   749 L      0.628         2.246
   770 A      1.000**       3.021
   771 W      1.000**       3.021
   775 L      0.998**       3.016
   776 H      0.740         2.479
   785 L      0.989*        2.999

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.06.98PB2.EU743784_)

            Pr(w>1)     post mean +- SE for w

     4 K      0.643         1.934 +- 0.761
    10 W      1.000**       2.506 +- 0.079
    15 T      0.998**       2.502 +- 0.108
    73 Y      1.000**       2.506 +- 0.079
   119 P      1.000**       2.506 +- 0.079
   120 T      1.000**       2.506 +- 0.080
   121 T      1.000**       2.506 +- 0.079
   122 S      1.000**       2.506 +- 0.079
   134 E      0.934         2.397 +- 0.391
   139 K      0.985*        2.480 +- 0.197
   140 Q      1.000**       2.506 +- 0.079
   143 Y      0.997**       2.502 +- 0.111
   153 P      0.904         2.349 +- 0.467
   155 N      0.999**       2.505 +- 0.091
   156 K      1.000**       2.506 +- 0.079
   157 T      1.000**       2.506 +- 0.079
   158 T      1.000**       2.506 +- 0.079
   168 V      1.000**       2.505 +- 0.086
   177 S      0.906         2.351 +- 0.471
   200 N      0.947         2.417 +- 0.356
   208 N      0.998**       2.504 +- 0.098
   247 G      0.813         2.203 +- 0.620
   249 T      0.994**       2.495 +- 0.144
   251 T      0.529         1.747 +- 0.800
   259 S      0.939         2.404 +- 0.383
   261 Q      1.000**       2.506 +- 0.079
   268 S      1.000**       2.506 +- 0.084
   276 H      1.000**       2.506 +- 0.079
   286 D      1.000**       2.506 +- 0.079
   292 R      0.523         1.739 +- 0.798
   294 Y      0.730         2.071 +- 0.707
   299 G      0.999**       2.504 +- 0.097
   300 T      1.000**       2.506 +- 0.079
   302 N      0.873         2.301 +- 0.524
   303 E      1.000**       2.506 +- 0.084
   306 K      1.000**       2.506 +- 0.079
   307 Q      1.000**       2.506 +- 0.079
   309 A      1.000**       2.506 +- 0.079
   310 K      1.000**       2.506 +- 0.079
   313 K      1.000**       2.506 +- 0.079
   315 H      0.965*        2.447 +- 0.296
   319 V      1.000**       2.506 +- 0.079
   323 S      1.000**       2.506 +- 0.084
   347 S      0.939         2.405 +- 0.382
   348 Q      1.000**       2.506 +- 0.079
   352 A      0.993**       2.494 +- 0.144
   354 T      1.000**       2.506 +- 0.079
   355 I      1.000**       2.506 +- 0.079
   357 S      1.000**       2.506 +- 0.079
   358 T      0.995**       2.498 +- 0.132
   374 G      0.858         2.276 +- 0.551
   385 S      1.000**       2.506 +- 0.079
   387 V      1.000**       2.506 +- 0.079
   389 N      0.711         2.041 +- 0.722
   391 L      1.000**       2.506 +- 0.079
   405 N      1.000**       2.506 +- 0.079
   406 T      1.000**       2.506 +- 0.079
   407 A      1.000**       2.506 +- 0.079
   409 T      0.776         2.145 +- 0.663
   442 R      0.921         2.376 +- 0.427
   456 I      0.965*        2.447 +- 0.296
   459 M      0.881         2.312 +- 0.514
   476 I      0.794         2.175 +- 0.639
   548 A      1.000**       2.506 +- 0.079
   553 S      1.000**       2.506 +- 0.082
   560 Y      1.000**       2.506 +- 0.079
   561 D      1.000**       2.506 +- 0.079
   562 T      1.000**       2.506 +- 0.079
   570 K      0.924         2.381 +- 0.422
   576 S      0.970*        2.453 +- 0.272
   580 D      1.000**       2.506 +- 0.079
   581 L      1.000**       2.506 +- 0.080
   584 G      1.000**       2.506 +- 0.079
   586 L      0.533         1.751 +- 0.804
   614 D      1.000**       2.506 +- 0.084
   617 N      0.587         1.847 +- 0.780
   661 T      1.000**       2.506 +- 0.080
   663 H      0.998**       2.502 +- 0.109
   664 Q      0.981*        2.475 +- 0.227
   686 V      1.000**       2.506 +- 0.079
   690 S      1.000**       2.506 +- 0.082
   696 A      1.000**       2.506 +- 0.080
   710 R      1.000**       2.506 +- 0.079
   726 G      1.000**       2.506 +- 0.079
   730 L      0.939         2.404 +- 0.392
   735 L      1.000**       2.505 +- 0.086
   739 Q      0.678         1.979 +- 0.759
   749 L      0.930         2.390 +- 0.408
   767 T      0.739         2.088 +- 0.695
   770 A      1.000**       2.506 +- 0.079
   771 W      1.000**       2.506 +- 0.079
   775 L      0.999**       2.505 +- 0.092
   776 H      0.953*        2.428 +- 0.337
   785 L      0.997**       2.502 +- 0.112