--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Jan 27 19:14:20 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_N1/GAG_1_2/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_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_N1/GAG_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -17418.94        -17467.06
2     -17416.52        -17465.71
--------------------------------------
TOTAL   -17417.13        -17466.60
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_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_N1/GAG_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}         3.664582    0.017174    3.415009    3.920539    3.661478   1363.17   1390.21    1.000
r(A<->C){all}   0.085815    0.000029    0.075024    0.095867    0.085780    699.61    731.79    1.000
r(A<->G){all}   0.325048    0.000258    0.294321    0.356344    0.324665    417.94    443.89    1.001
r(A<->T){all}   0.047500    0.000017    0.039042    0.055214    0.047451    580.17    764.70    1.001
r(C<->G){all}   0.045901    0.000027    0.035866    0.055888    0.045822    569.97    690.70    1.000
r(C<->T){all}   0.429957    0.000315    0.394593    0.463562    0.430299    399.84    448.78    1.001
r(G<->T){all}   0.065779    0.000040    0.054040    0.079132    0.065706    664.68    778.67    1.001
pi(A){all}      0.414011    0.000091    0.395456    0.432463    0.413935    733.21    788.57    1.000
pi(C){all}      0.196870    0.000060    0.181473    0.211808    0.196789    647.45    727.51    1.003
pi(G){all}      0.211998    0.000059    0.196424    0.225968    0.211954    397.34    552.99    1.004
pi(T){all}      0.177121    0.000053    0.163057    0.191572    0.177010    529.57    625.78    1.000
alpha{1,2}      0.316913    0.000474    0.275851    0.361655    0.316001    941.95   1078.66    1.000
alpha{3}        2.280095    0.089029    1.745101    2.915918    2.261138   1244.40   1329.12    1.000
pinvar{all}     0.177769    0.000546    0.128612    0.219657    0.177672    947.50   1073.38    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	-15746.913577
Model 2: PositiveSelection	-15685.569871
Model 0: one-ratio	-16603.611266
Model 3: discrete	-15606.785351
Model 7: beta	-15645.983528
Model 8: beta&w>1	-15582.541691


Model 0 vs 1	1713.395378000001

Model 2 vs 1	122.68741199999931

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.CM.07.BS65.JX244941_)

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

    13 A      0.635         2.046
    26 K      0.988*        2.626
    29 L      0.746         2.229
    65 A      0.845         2.392
    77 Y      0.999**       2.645
    82 T      0.997**       2.641
    88 Q      0.877         2.444
    89 R      1.000**       2.647
    91 E      0.763         2.256
   125 T      0.829         2.366
   133 P      1.000**       2.646
   202 V      0.977*        2.608
   210 N      0.987*        2.625
   229 N      0.512         1.843
   239 S      1.000**       2.647
   344 S      0.913         2.503
   359 Q      1.000**       2.646
   360 G      0.612         2.008
   434 S      0.878         2.446
   454 V      0.999**       2.646

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.CM.07.BS65.JX244941_)

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

    13 A      0.651         1.977 +- 0.716
    26 K      0.984*        2.485 +- 0.214
    29 L      0.723         2.087 +- 0.675
    65 A      0.811         2.223 +- 0.595
    77 Y      0.999**       2.508 +- 0.112
    82 T      0.995**       2.502 +- 0.146
    88 Q      0.864         2.300 +- 0.520
    89 R      1.000**       2.510 +- 0.099
    91 E      0.748         2.124 +- 0.655
   125 T      0.798         2.202 +- 0.610
   133 P      1.000**       2.509 +- 0.103
   202 V      0.968*        2.462 +- 0.282
   210 N      0.981*        2.482 +- 0.225
   239 S      1.000**       2.510 +- 0.100
   344 S      0.893         2.347 +- 0.473
   359 Q      1.000**       2.510 +- 0.101
   360 G      0.590         1.887 +- 0.740
   434 S      0.862         2.297 +- 0.524
   454 V      0.999**       2.509 +- 0.108


Model 8 vs 7	126.88367400000061

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.CM.07.BS65.JX244941_)

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

    13 A      0.946         1.987
    26 K      0.998**       2.051
    28 K      0.796         1.800
    29 L      0.937         1.975
    65 A      0.964*        2.009
    73 V      0.756         1.745
    77 Y      1.000**       2.054
    82 T      0.999**       2.053
    88 Q      0.978*        2.027
    89 R      1.000**       2.054
    91 E      0.953*        1.996
   111 D      0.656         1.622
   114 H      0.820         1.829
   125 T      0.961*        2.005
   133 P      1.000**       2.054
   134 L      0.760         1.756
   202 V      0.995**       2.048
   210 N      0.997**       2.051
   229 N      0.848         1.864
   239 S      1.000**       2.054
   267 V      0.545         1.477
   344 S      0.982*        2.032
   359 Q      1.000**       2.054
   360 G      0.901         1.930
   374 I      0.757         1.750
   434 S      0.978*        2.027
   454 V      1.000**       2.054

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.CM.07.BS65.JX244941_)

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

    13 A      0.533         1.767 +- 0.785
    26 K      0.986*        2.479 +- 0.181
    29 L      0.720         2.057 +- 0.711
    65 A      0.892         2.329 +- 0.492
    73 V      0.523         1.729 +- 0.811
    77 Y      1.000**       2.499 +- 0.032
    82 T      0.998**       2.497 +- 0.073
    88 Q      0.840         2.249 +- 0.576
    89 R      1.000**       2.500 +- 0.001
    91 E      0.730         2.074 +- 0.701
   125 T      0.863         2.283 +- 0.545
   133 P      1.000**       2.500 +- 0.017
   202 V      0.982*        2.471 +- 0.212
   210 N      0.989*        2.483 +- 0.162
   229 N      0.582         1.832 +- 0.790
   239 S      1.000**       2.500 +- 0.011
   344 S      0.927         2.385 +- 0.410
   359 Q      1.000**       2.500 +- 0.015
   360 G      0.620         1.897 +- 0.771
   434 S      0.872         2.298 +- 0.527
   454 V      1.000**       2.499 +- 0.029