--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Jan 28 05:01:24 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_3/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -17439.59        -17491.80
2     -17441.55        -17483.87
--------------------------------------
TOTAL   -17440.15        -17491.10
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         3.665210    0.017469    3.408917    3.924786    3.663371   1014.55   1113.01    1.000
r(A<->C){all}   0.085257    0.000028    0.074599    0.095353    0.085191    578.37    693.04    1.000
r(A<->G){all}   0.302350    0.000248    0.271668    0.333539    0.302333    174.99    217.26    1.001
r(A<->T){all}   0.043506    0.000016    0.036205    0.051691    0.043459    857.04    872.90    1.002
r(C<->G){all}   0.050841    0.000028    0.041122    0.061631    0.050633    840.14    843.58    1.000
r(C<->T){all}   0.451794    0.000330    0.414924    0.485958    0.451815    183.58    227.23    1.001
r(G<->T){all}   0.066252    0.000041    0.053859    0.078976    0.066211    616.08    649.30    1.005
pi(A){all}      0.413172    0.000089    0.394282    0.431264    0.413102    711.07    730.52    1.000
pi(C){all}      0.200829    0.000057    0.186678    0.216176    0.200821    504.44    578.66    1.000
pi(G){all}      0.208460    0.000063    0.192474    0.223696    0.208426    554.04    623.38    1.000
pi(T){all}      0.177539    0.000058    0.162696    0.192125    0.177546    446.82    521.37    1.000
alpha{1,2}      0.327520    0.000451    0.286598    0.368909    0.326647   1070.34   1132.39    1.000
alpha{3}        2.546008    0.106460    1.945496    3.213376    2.528353   1335.19   1338.71    1.000
pinvar{all}     0.199450    0.000453    0.159863    0.243377    0.199033   1075.99   1136.74    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	-15404.232647
Model 2: PositiveSelection	-15340.797519
Model 0: one-ratio	-16230.792918
Model 3: discrete	-15268.416895
Model 7: beta	-15312.704747
Model 8: beta&w>1	-15254.597723


Model 0 vs 1	1653.120541999997

Model 2 vs 1	126.87025600000197

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: B.CY.07.CY201.JF683753_)

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

    77 Y      1.000**       3.067
    82 V      1.000**       3.067
    89 K      1.000**       3.067
    91 E      0.972*        3.010
   113 A      0.976*        3.017
   134 P      1.000**       3.067
   203 L      0.966*        2.996
   211 I      0.684         2.414
   240 N      0.997**       3.062
   320 T      0.611         2.264
   345 S      0.995**       3.058
   360 N      1.000**       3.067
   371 Q      0.931         2.924
   447 Q      0.594         2.229
   452 S      0.945         2.954

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: B.CY.07.CY201.JF683753_)

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

    77 Y      1.000**       3.326 +- 0.379
    82 V      1.000**       3.326 +- 0.380
    89 K      1.000**       3.326 +- 0.379
    91 E      0.957*        3.221 +- 0.602
   113 A      0.968*        3.248 +- 0.556
   134 P      1.000**       3.326 +- 0.379
   203 L      0.959*        3.228 +- 0.593
   211 I      0.588         2.329 +- 1.159
   240 N      0.997**       3.319 +- 0.400
   320 T      0.549         2.248 +- 1.172
   345 S      0.995**       3.315 +- 0.411
   360 N      1.000**       3.326 +- 0.380
   371 Q      0.923         3.143 +- 0.721
   447 Q      0.546         2.244 +- 1.176
   452 S      0.934         3.168 +- 0.686


Model 8 vs 7	116.214047999998

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: B.CY.07.CY201.JF683753_)

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

    77 Y      1.000**       2.453
    82 V      1.000**       2.453
    88 Q      0.515         1.695
    89 K      1.000**       2.453
    91 E      0.981*        2.423
   113 A      0.983*        2.427
   134 P      1.000**       2.453
   203 L      0.976*        2.415
   211 I      0.813         2.161
   240 N      0.998**       2.449
   320 T      0.767         2.087
   345 S      0.997**       2.447
   360 N      1.000**       2.452
   371 Q      0.942         2.363
   447 Q      0.720         2.011
   452 S      0.968*        2.402

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: B.CY.07.CY201.JF683753_)

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

    77 Y      1.000**       2.500 +- 0.005
    82 V      1.000**       2.500 +- 0.013
    88 Q      0.551         1.791 +- 0.787
    89 K      1.000**       2.500 +- 0.006
    91 E      0.982*        2.472 +- 0.208
   113 A      0.985*        2.477 +- 0.188
   134 P      1.000**       2.500 +- 0.006
   203 L      0.979*        2.468 +- 0.223
   211 I      0.842         2.251 +- 0.577
   240 N      0.998**       2.496 +- 0.074
   320 T      0.811         2.200 +- 0.624
   345 S      0.997**       2.495 +- 0.086
   360 N      1.000**       2.500 +- 0.023
   371 Q      0.954*        2.427 +- 0.331
   447 Q      0.775         2.140 +- 0.669
   452 S      0.973*        2.458 +- 0.254