--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Jan 28 15:22:51 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_4/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_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/GAG_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -18563.06        -18609.94
2     -18560.26        -18609.34
--------------------------------------
TOTAL   -18560.90        -18609.68
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_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/GAG_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}         4.047602    0.021180    3.749631    4.316541    4.044593   1167.01   1237.70    1.000
r(A<->C){all}   0.087265    0.000031    0.076137    0.097434    0.086955    496.04    647.34    1.001
r(A<->G){all}   0.288364    0.000218    0.259681    0.317692    0.288284    449.92    476.72    1.002
r(A<->T){all}   0.049655    0.000018    0.041478    0.058003    0.049512    820.79    867.19    1.000
r(C<->G){all}   0.049329    0.000028    0.039305    0.059497    0.049335    782.67    812.62    1.000
r(C<->T){all}   0.463656    0.000303    0.426399    0.494098    0.464161    399.58    438.34    1.003
r(G<->T){all}   0.061732    0.000037    0.050452    0.073845    0.061484    736.06    775.27    1.005
pi(A){all}      0.410053    0.000087    0.393082    0.429530    0.410030    807.71    820.71    1.000
pi(C){all}      0.194451    0.000064    0.179174    0.210071    0.194309    580.42    597.49    1.001
pi(G){all}      0.221123    0.000061    0.205993    0.236699    0.221005    611.18    694.84    1.002
pi(T){all}      0.174373    0.000053    0.160729    0.189275    0.174110    612.85    689.82    1.000
alpha{1,2}      0.336032    0.000478    0.295830    0.380006    0.335225    914.10   1127.34    1.000
alpha{3}        2.013847    0.055361    1.605846    2.513976    1.998117    976.26   1191.06    1.000
pinvar{all}     0.196280    0.000494    0.153741    0.239883    0.196791    846.07    955.12    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	-16074.737989
Model 2: PositiveSelection	-15994.902025
Model 0: one-ratio	-17007.678345
Model 3: discrete	-15927.984812
Model 7: beta	-15982.055321
Model 8: beta&w>1	-15908.915041


Model 0 vs 1	1865.880712000002

Model 2 vs 1	159.67192799999975

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: A1.KE.94.clone_904.GQ430768_)

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

    28 Q      1.000**       3.029
    69 G      0.975*        2.978
    79 F      1.000**       3.029
    84 T      1.000**       3.029
    91 R      0.999**       3.027
    93 E      0.916         2.858
   137 S      0.999**       3.027
   206 T      0.804         2.631
   214 I      0.999**       3.028
   243 S      1.000**       3.029
   271 V      0.917         2.861
   294 T      0.937         2.901
   323 S      0.995**       3.020
   348 G      0.999**       3.027
   361 V      0.671         2.361
   363 Q      1.000**       3.029
   449 Q      0.998**       3.026
   454 V      0.999**       3.028

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: A1.KE.94.clone_904.GQ430768_)

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

    28 Q      1.000**       3.416 +- 0.278
    69 G      0.962*        3.324 +- 0.535
    79 F      1.000**       3.416 +- 0.279
    84 T      1.000**       3.416 +- 0.278
    91 R      0.998**       3.412 +- 0.294
    93 E      0.794         2.904 +- 1.007
   137 S      0.999**       3.413 +- 0.290
   206 T      0.680         2.630 +- 1.146
   214 I      0.999**       3.414 +- 0.285
   243 S      1.000**       3.415 +- 0.282
   271 V      0.857         3.064 +- 0.885
   294 T      0.879         3.118 +- 0.831
   323 S      0.994**       3.403 +- 0.330
   348 G      0.999**       3.413 +- 0.290
   363 Q      1.000**       3.416 +- 0.277
   449 Q      0.998**       3.412 +- 0.296
   454 V      0.999**       3.415 +- 0.284


Model 8 vs 7	146.28055999999924

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: A1.KE.94.clone_904.GQ430768_)

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

    28 Q      1.000**       2.448
    69 G      0.983*        2.421
    79 F      1.000**       2.448
    84 T      1.000**       2.448
    91 R      0.999**       2.446
    93 E      0.951*        2.370
   137 S      0.999**       2.447
   206 T      0.876         2.251
   210 Q      0.554         1.742
   214 I      0.999**       2.447
   243 S      1.000**       2.447
   271 V      0.958*        2.382
   294 T      0.968*        2.398
   323 S      0.997**       2.443
   348 G      0.999**       2.447
   361 V      0.821         2.167
   363 Q      1.000**       2.448
   449 Q      0.999**       2.446
   454 V      1.000**       2.447

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: A1.KE.94.clone_904.GQ430768_)

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

    28 Q      1.000**       2.500 +- 0.018
    69 G      0.979*        2.468 +- 0.224
    79 F      1.000**       2.500 +- 0.023
    84 T      1.000**       2.500 +- 0.016
    91 R      0.998**       2.497 +- 0.064
    93 E      0.932         2.393 +- 0.396
   137 S      0.999**       2.498 +- 0.052
   206 T      0.860         2.278 +- 0.551
   210 Q      0.516         1.731 +- 0.796
   214 I      0.999**       2.499 +- 0.043
   243 S      1.000**       2.499 +- 0.034
   271 V      0.950*        2.422 +- 0.343
   294 T      0.960*        2.437 +- 0.308
   323 S      0.996**       2.494 +- 0.097
   348 G      0.999**       2.498 +- 0.050
   361 V      0.743         2.097 +- 0.686
   363 Q      1.000**       2.500 +- 0.003
   449 Q      0.998**       2.497 +- 0.065
   454 V      0.999**       2.499 +- 0.036