--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Jan 26 01:38:09 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_N1/ENV_1_4/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_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/ADOPS/HIV1_N1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -47574.84        -47619.35
2     -47575.23        -47618.20
--------------------------------------
TOTAL   -47575.02        -47618.93
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_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/ADOPS/HIV1_N1/ENV_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}         7.748828    0.046437    7.351036    8.165507    7.745057   1022.37   1037.23    1.000
r(A<->C){all}   0.130021    0.000025    0.120680    0.139947    0.129875    429.33    460.64    1.002
r(A<->G){all}   0.302603    0.000117    0.280696    0.322816    0.302699    235.43    263.58    1.014
r(A<->T){all}   0.060401    0.000010    0.054216    0.066392    0.060381    506.54    673.28    1.000
r(C<->G){all}   0.069583    0.000025    0.059879    0.079438    0.069256    434.43    473.34    1.002
r(C<->T){all}   0.339722    0.000133    0.318179    0.362378    0.339234    247.05    307.01    1.017
r(G<->T){all}   0.097670    0.000023    0.088453    0.107563    0.097525    287.68    470.99    1.003
pi(A){all}      0.387628    0.000047    0.374024    0.400839    0.387767    454.91    455.51    1.000
pi(C){all}      0.182606    0.000024    0.172544    0.191875    0.182592    342.98    402.93    1.008
pi(G){all}      0.213580    0.000029    0.202984    0.224087    0.213451    356.18    377.00    1.017
pi(T){all}      0.216186    0.000035    0.205095    0.228336    0.216252    371.90    396.89    1.005
alpha{1,2}      0.467455    0.000489    0.426679    0.511776    0.466613   1148.31   1172.51    1.000
alpha{3}        1.074649    0.005165    0.944838    1.223442    1.070980   1013.18   1226.76    1.000
pinvar{all}     0.175622    0.000208    0.147828    0.202891    0.175615   1041.35   1121.90    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	-37442.164166
Model 2: PositiveSelection	-36887.367584
Model 0: one-ratio	-39726.536894
Model 3: discrete	-36879.498558
Model 7: beta	-37287.202195
Model 8: beta&w>1	-36784.671892


Model 0 vs 1	4568.74545599999

Model 2 vs 1	1109.5931640000053

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 02_AG.US.01.APV_12.DQ869018_)

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

     7 Y      1.000**       3.581
     9 C      0.852         3.201
    12 I      0.883         3.281
    74 H      1.000**       3.582
   120 Q      1.000**       3.582
   121 D      0.985*        3.543
   122 F      1.000**       3.582
   123 M      1.000**       3.582
   132 I      0.998**       3.577
   140 R      1.000**       3.582
   154 D      0.673         2.738
   155 S      1.000**       3.582
   165 A      0.846         3.184
   247 T      0.555         2.432
   257 K      0.997**       3.574
   264 G      0.968*        3.499
   272 R      1.000**       3.582
   283 D      1.000**       3.582
   297 K      0.764         2.971
   298 A      1.000**       3.582
   299 Q      1.000**       3.582
   302 K      1.000**       3.582
   305 Q      1.000**       3.582
   306 E      1.000**       3.582
   308 A      1.000**       3.582
   309 K      1.000**       3.582
   319 N      1.000**       3.582
   321 N      1.000**       3.582
   322 K      1.000**       3.581
   348 A      1.000**       3.582
   352 T      1.000**       3.582
   353 I      1.000**       3.582
   355 D      1.000**       3.582
   382 A      1.000**       3.582
   384 E      1.000**       3.582
   388 E      0.987*        3.548
   402 N      1.000**       3.582
   403 S      0.785         3.027
   438 R      0.787         3.033
   543 D      0.728         2.881
   548 S      0.998**       3.576
   554 Y      1.000**       3.582
   555 N      1.000**       3.582
   556 D      0.617         2.592
   572 S      1.000**       3.582
   601 S      1.000**       3.582
   647 P      0.841         3.171
   648 T      1.000**       3.581
   650 H      1.000**       3.581
   651 Q      0.999**       3.580
   673 V      1.000**       3.582
   683 A      1.000**       3.582
   697 R      0.703         2.814
   711 A      0.979*        3.526
   720 S      0.839         3.166
   747 I      0.726         2.875
   751 T      0.999**       3.580
   752 G      0.965*        3.492
   756 R      0.996**       3.571
   766 L      0.998**       3.575

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: 02_AG.US.01.APV_12.DQ869018_)

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

     7 Y      1.000**       3.500 +- 0.027
     9 C      0.877         3.191 +- 0.822
    12 I      0.901         3.254 +- 0.745
    74 H      1.000**       3.500 +- 0.001
   120 Q      1.000**       3.500 +- 0.000
   121 D      0.988*        3.471 +- 0.267
   122 F      1.000**       3.500 +- 0.000
   123 M      1.000**       3.500 +- 0.000
   132 I      0.999**       3.496 +- 0.095
   140 R      1.000**       3.500 +- 0.017
   154 D      0.740         2.849 +- 1.097
   155 S      1.000**       3.500 +- 0.000
   165 A      0.866         3.165 +- 0.852
   247 T      0.616         2.539 +- 1.216
   257 K      0.997**       3.494 +- 0.127
   264 G      0.974*        3.434 +- 0.400
   272 R      1.000**       3.500 +- 0.002
   283 D      1.000**       3.500 +- 0.002
   297 K      0.814         3.034 +- 0.974
   298 A      1.000**       3.500 +- 0.000
   299 Q      1.000**       3.500 +- 0.000
   302 K      1.000**       3.500 +- 0.001
   305 Q      1.000**       3.500 +- 0.001
   306 E      1.000**       3.500 +- 0.005
   308 A      1.000**       3.500 +- 0.000
   309 K      1.000**       3.500 +- 0.002
   319 N      1.000**       3.500 +- 0.001
   321 N      1.000**       3.500 +- 0.019
   322 K      1.000**       3.499 +- 0.049
   348 A      1.000**       3.500 +- 0.000
   352 T      1.000**       3.500 +- 0.000
   353 I      1.000**       3.500 +- 0.000
   355 D      1.000**       3.500 +- 0.000
   382 A      1.000**       3.500 +- 0.002
   384 E      1.000**       3.500 +- 0.000
   388 E      0.989*        3.473 +- 0.258
   402 N      1.000**       3.500 +- 0.000
   403 S      0.822         3.056 +- 0.956
   438 R      0.826         3.066 +- 0.947
   543 D      0.769         2.923 +- 1.053
   548 S      0.998**       3.495 +- 0.111
   554 Y      1.000**       3.500 +- 0.000
   555 N      1.000**       3.500 +- 0.000
   556 D      0.679         2.698 +- 1.167
   572 S      1.000**       3.500 +- 0.000
   601 S      1.000**       3.500 +- 0.002
   647 P      0.862         3.156 +- 0.861
   648 T      1.000**       3.500 +- 0.035
   650 H      1.000**       3.499 +- 0.052
   651 Q      0.999**       3.499 +- 0.056
   673 V      1.000**       3.500 +- 0.002
   683 A      1.000**       3.500 +- 0.004
   697 R      0.734         2.834 +- 1.105
   711 A      0.981*        3.453 +- 0.339
   720 S      0.857         3.143 +- 0.875
   747 I      0.781         2.952 +- 1.034
   751 T      0.999**       3.498 +- 0.061
   752 G      0.970*        3.425 +- 0.426
   756 R      0.996**       3.491 +- 0.154
   766 L      0.998**       3.494 +- 0.118


Model 8 vs 7	1005.0606059999991

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 02_AG.US.01.APV_12.DQ869018_)

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

     7 Y      1.000**       3.160
     9 C      0.865         2.862
    12 I      0.899         2.936
    74 H      1.000**       3.160
   120 Q      1.000**       3.160
   121 D      0.982*        3.121
   122 F      1.000**       3.160
   123 M      1.000**       3.160
   132 I      0.998**       3.155
   140 R      1.000**       3.160
   154 D      0.674         2.444
   155 S      1.000**       3.160
   165 A      0.877         2.888
   247 T      0.633         2.349
   257 K      0.996**       3.150
   264 G      0.968*        3.089
   272 R      1.000**       3.160
   283 D      1.000**       3.160
   297 K      0.783         2.683
   298 A      1.000**       3.160
   299 Q      1.000**       3.160
   302 K      1.000**       3.160
   305 Q      1.000**       3.160
   306 E      1.000**       3.160
   308 A      1.000**       3.160
   309 K      1.000**       3.160
   319 N      1.000**       3.160
   321 N      1.000**       3.160
   322 K      0.999**       3.159
   348 A      1.000**       3.160
   352 T      1.000**       3.160
   353 I      1.000**       3.160
   355 D      1.000**       3.160
   382 A      1.000**       3.160
   384 E      1.000**       3.160
   388 E      0.986*        3.129
   402 N      1.000**       3.160
   403 S      0.795         2.707
   438 R      0.810         2.742
   543 D      0.773         2.658
   548 S      0.998**       3.155
   554 Y      1.000**       3.160
   555 N      1.000**       3.160
   556 D      0.648         2.385
   572 S      1.000**       3.160
   601 S      1.000**       3.160
   647 P      0.871         2.874
   648 T      1.000**       3.159
   650 H      0.999**       3.159
   651 Q      0.999**       3.159
   673 V      1.000**       3.160
   683 A      1.000**       3.160
   697 R      0.756         2.617
   711 A      0.982*        3.120
   720 S      0.851         2.829
   747 I      0.753         2.617
   751 T      0.999**       3.158
   752 G      0.968*        3.089
   756 R      0.996**       3.151
   766 L      0.997**       3.153

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: 02_AG.US.01.APV_12.DQ869018_)

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

     7 Y      1.000**       3.499 +- 0.042
     9 C      0.618         2.519 +- 1.249
    12 I      0.713         2.761 +- 1.164
    74 H      1.000**       3.500 +- 0.001
   120 Q      1.000**       3.500 +- 0.001
   121 D      0.924         3.306 +- 0.677
   122 F      1.000**       3.500 +- 0.001
   123 M      1.000**       3.500 +- 0.001
   132 I      0.993**       3.483 +- 0.210
   140 R      1.000**       3.500 +- 0.033
   155 S      1.000**       3.500 +- 0.001
   165 A      0.689         2.700 +- 1.192
   257 K      0.985*        3.463 +- 0.306
   264 G      0.891         3.220 +- 0.800
   272 R      1.000**       3.500 +- 0.003
   283 D      1.000**       3.500 +- 0.004
   298 A      1.000**       3.500 +- 0.001
   299 Q      1.000**       3.500 +- 0.001
   302 K      1.000**       3.500 +- 0.002
   305 Q      1.000**       3.500 +- 0.002
   306 E      1.000**       3.500 +- 0.008
   308 A      1.000**       3.500 +- 0.001
   309 K      1.000**       3.500 +- 0.003
   319 N      1.000**       3.500 +- 0.002
   321 N      1.000**       3.499 +- 0.039
   322 K      0.998**       3.496 +- 0.102
   348 A      1.000**       3.500 +- 0.001
   352 T      1.000**       3.500 +- 0.001
   353 I      1.000**       3.500 +- 0.001
   355 D      1.000**       3.500 +- 0.001
   382 A      1.000**       3.500 +- 0.004
   384 E      1.000**       3.500 +- 0.001
   388 E      0.953*        3.379 +- 0.544
   402 N      1.000**       3.500 +- 0.001
   548 S      0.995**       3.488 +- 0.178
   554 Y      1.000**       3.500 +- 0.001
   555 N      1.000**       3.500 +- 0.001
   572 S      1.000**       3.500 +- 0.001
   601 S      1.000**       3.500 +- 0.004
   647 P      0.668         2.645 +- 1.213
   648 T      1.000**       3.499 +- 0.049
   650 H      0.999**       3.497 +- 0.088
   651 Q      0.999**       3.497 +- 0.084
   673 V      1.000**       3.500 +- 0.004
   683 A      1.000**       3.500 +- 0.005
   711 A      0.953*        3.378 +- 0.546
   720 S      0.654         2.608 +- 1.227
   751 T      0.998**       3.495 +- 0.114
   752 G      0.908         3.265 +- 0.741
   756 R      0.992**       3.481 +- 0.223
   766 L      0.993**       3.481 +- 0.218