--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Jan 27 09:17:35 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/GAG_1_1/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_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_N1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -18272.33        -18319.14
2     -18273.56        -18313.19
--------------------------------------
TOTAL   -18272.77        -18318.45
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_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_N1/GAG_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}         3.935340    0.019459    3.659520    4.203024    3.935345   1223.88   1300.51    1.000
r(A<->C){all}   0.087036    0.000029    0.077142    0.098518    0.086923    708.97    716.90    1.000
r(A<->G){all}   0.309475    0.000224    0.279997    0.337671    0.309110    296.43    386.32    1.000
r(A<->T){all}   0.045167    0.000017    0.037245    0.053086    0.045104    667.74    836.36    1.000
r(C<->G){all}   0.043314    0.000025    0.033523    0.052731    0.043060    565.03    718.61    1.000
r(C<->T){all}   0.435891    0.000308    0.400834    0.467960    0.436154    307.19    373.02    1.000
r(G<->T){all}   0.079117    0.000048    0.065913    0.092391    0.079029    614.51    669.83    1.000
pi(A){all}      0.398392    0.000080    0.381733    0.416692    0.398541    763.25    774.72    1.000
pi(C){all}      0.205047    0.000057    0.190982    0.220586    0.204874    534.57    687.05    1.000
pi(G){all}      0.218028    0.000061    0.203262    0.233594    0.217976    532.13    591.87    1.000
pi(T){all}      0.178532    0.000051    0.163902    0.191875    0.178439    476.21    599.20    1.000
alpha{1,2}      0.342905    0.000510    0.297558    0.384129    0.341400   1003.47   1088.03    1.000
alpha{3}        1.906849    0.051151    1.461061    2.325904    1.897151   1414.61   1433.47    1.000
pinvar{all}     0.162694    0.000527    0.117398    0.206237    0.163032    958.43   1067.22    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	-16324.941755
Model 2: PositiveSelection	-16268.105319
Model 0: one-ratio	-17178.663071
Model 3: discrete	-16203.783623
Model 7: beta	-16231.126789
Model 8: beta&w>1	-16173.827495


Model 0 vs 1	1707.4426319999984

Model 2 vs 1	113.67287199999919

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: BC.CN.07.07CNYN367.KF835544_)

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

    77 Y      0.973*        2.688
    82 T      1.000**       2.734
    89 G      0.999**       2.733
    91 E      0.854         2.481
   115 T      1.000**       2.735
   134 P      0.993**       2.723
   201 T      0.987*        2.712
   209 V      0.920         2.595
   238 S      1.000**       2.734
   358 S      1.000**       2.734
   359 A      0.987*        2.713
   370 P      0.530         1.919
   424 H      0.778         2.350
   445 S      0.725         2.258
   451 P      0.998**       2.731
   455 P      0.986*        2.711
   457 L      0.572         1.993
   458 T      0.580         2.006

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: BC.CN.07.07CNYN367.KF835544_)

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

    77 Y      0.968*        2.469 +- 0.299
    82 T      1.000**       2.518 +- 0.134
    89 G      0.999**       2.517 +- 0.143
    91 E      0.874         2.320 +- 0.510
   115 T      1.000**       2.518 +- 0.134
   116 I      0.529         1.797 +- 0.755
   134 P      0.991**       2.504 +- 0.196
   201 T      0.983*        2.493 +- 0.235
   209 V      0.919         2.393 +- 0.430
   238 S      0.999**       2.517 +- 0.139
   358 S      1.000**       2.518 +- 0.137
   359 A      0.985*        2.496 +- 0.225
   370 P      0.561         1.846 +- 0.751
   424 H      0.797         2.203 +- 0.615
   445 S      0.754         2.138 +- 0.654
   451 P      0.997**       2.514 +- 0.156
   455 P      0.982*        2.491 +- 0.242
   457 L      0.606         1.913 +- 0.740
   458 T      0.613         1.925 +- 0.737


Model 8 vs 7	114.59858800000075

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: BC.CN.07.07CNYN367.KF835544_)

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

    13 K      0.692         1.767
    65 A      0.517         1.527
    77 Y      0.988*        2.148
    82 T      1.000**       2.163
    89 G      1.000**       2.162
    91 E      0.954*        2.104
   115 T      1.000**       2.163
   116 I      0.771         1.864
   126 L      0.685         1.754
   134 P      0.997**       2.159
   201 T      0.993**       2.154
   209 V      0.971*        2.125
   238 S      1.000**       2.163
   266 T      0.547         1.567
   358 S      1.000**       2.163
   359 A      0.994**       2.156
   370 P      0.746         1.831
   424 H      0.914         2.051
   445 S      0.900         2.033
   451 P      0.999**       2.161
   455 P      0.993**       2.153
   457 L      0.812         1.919
   458 T      0.832         1.944

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: BC.CN.07.07CNYN367.KF835544_)

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

    77 Y      0.982*        2.471 +- 0.212
    82 T      1.000**       2.500 +- 0.007
    89 G      0.999**       2.499 +- 0.042
    91 E      0.865         2.288 +- 0.536
   115 T      1.000**       2.500 +- 0.005
   116 I      0.618         1.892 +- 0.774
   134 P      0.996**       2.494 +- 0.099
   201 T      0.990*        2.484 +- 0.158
   209 V      0.938         2.403 +- 0.378
   238 S      1.000**       2.499 +- 0.031
   358 S      1.000**       2.500 +- 0.025
   359 A      0.989*        2.483 +- 0.163
   370 P      0.576         1.826 +- 0.788
   424 H      0.809         2.199 +- 0.620
   445 S      0.775         2.145 +- 0.659
   451 P      0.999**       2.498 +- 0.058
   455 P      0.990*        2.484 +- 0.157
   457 L      0.658         1.958 +- 0.753
   458 T      0.692         2.011 +- 0.733