--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Mar 20 06:56:20 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/GAG_1_5/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_1_5/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/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -18327.21        -18371.35
2     -18328.67        -18370.91
--------------------------------------
TOTAL   -18327.69        -18371.15
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_1_5/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/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         3.935858    0.019342    3.659284    4.208033    3.934342    802.94    953.12    1.001
r(A<->C){all}   0.091202    0.000032    0.080702    0.102607    0.091094    625.31    741.28    1.000
r(A<->G){all}   0.312617    0.000242    0.282560    0.341310    0.312783    425.33    432.79    1.000
r(A<->T){all}   0.045048    0.000017    0.036403    0.052688    0.044911    833.07    840.70    1.001
r(C<->G){all}   0.048697    0.000026    0.038817    0.057999    0.048721    599.23    717.89    1.000
r(C<->T){all}   0.428210    0.000306    0.395412    0.463020    0.428166    402.35    415.21    1.000
r(G<->T){all}   0.074225    0.000043    0.061397    0.086894    0.073858    635.35    738.43    1.000
pi(A){all}      0.398270    0.000084    0.380658    0.416867    0.398367    611.99    737.75    1.000
pi(C){all}      0.206623    0.000065    0.191095    0.222220    0.206496    477.62    519.09    1.000
pi(G){all}      0.214060    0.000060    0.199768    0.229666    0.214065    562.29    621.94    1.000
pi(T){all}      0.181047    0.000057    0.166452    0.195647    0.180959    693.59    749.56    1.000
alpha{1,2}      0.300114    0.000378    0.263201    0.337521    0.299038   1048.79   1189.67    1.000
alpha{3}        1.736297    0.040599    1.361735    2.131270    1.724120   1168.17   1203.51    1.001
pinvar{all}     0.149418    0.000584    0.101102    0.195927    0.149388   1075.33   1103.82    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	-15275.88814
Model 2: PositiveSelection	-15214.968097
Model 0: one-ratio	-16149.492641
Model 3: discrete	-15140.327268
Model 7: beta	-15179.162644
Model 8: beta&w>1	-15120.366518


Model 0 vs 1	1747.2090020000032

Model 2 vs 1	121.84008599999652

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.00.C015F1P190.GU458453_)

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

    28 Q      0.774         2.461
    59 I      0.984*        2.858
    65 T      0.982*        2.854
    77 Y      0.985*        2.860
    82 T      1.000**       2.888
    89 R      1.000**       2.888
    91 D      0.608         2.148
   129 S      0.999**       2.887
   198 V      0.999**       2.887
   206 I      0.976*        2.842
   235 S      1.000**       2.888
   354 A      0.949         2.792
   355 N      1.000**       2.887
   441 V      0.758         2.431

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.00.C015F1P190.GU458453_)

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

    28 Q      0.753         2.218 +- 0.750
    59 I      0.979*        2.707 +- 0.491
    65 T      0.978*        2.711 +- 0.498
    77 Y      0.982*        2.718 +- 0.487
    82 T      1.000**       2.749 +- 0.433
    89 R      1.000**       2.749 +- 0.433
    91 D      0.630         2.000 +- 0.798
   129 S      0.999**       2.748 +- 0.436
   198 V      0.999**       2.748 +- 0.435
   206 I      0.971*        2.696 +- 0.514
   235 S      1.000**       2.749 +- 0.433
   354 A      0.937         2.617 +- 0.584
   355 N      0.999**       2.748 +- 0.435
   441 V      0.746         2.253 +- 0.803


Model 8 vs 7	117.59225199999855

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.00.C015F1P190.GU458453_)

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

    28 Q      0.923         2.200
    59 I      0.993**       2.303
    65 T      0.992**       2.301
    77 Y      0.993**       2.302
    82 T      1.000**       2.312
    89 R      1.000**       2.312
    91 D      0.842         2.082
   129 S      1.000**       2.312
   198 V      1.000**       2.312
   206 I      0.990*        2.298
   235 S      1.000**       2.312
   354 A      0.983*        2.287
   355 N      1.000**       2.312
   441 V      0.903         2.171

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.00.C015F1P190.GU458453_)

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

    28 Q      0.833         2.238 +- 0.585
    59 I      0.988*        2.481 +- 0.173
    65 T      0.991**       2.486 +- 0.150
    77 Y      0.992**       2.487 +- 0.143
    82 T      1.000**       2.500 +- 0.006
    89 R      1.000**       2.500 +- 0.015
    91 D      0.734         2.081 +- 0.697
   129 S      1.000**       2.499 +- 0.030
   198 V      1.000**       2.499 +- 0.032
   206 I      0.986*        2.477 +- 0.187
   235 S      1.000**       2.500 +- 0.003
   354 A      0.967*        2.448 +- 0.280
   355 N      1.000**       2.499 +- 0.030
   441 V      0.872         2.297 +- 0.530