--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Mar 24 14:59:40 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=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS1/HIV1_AMINO/POL_1_5/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/HIV1_AMINO/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/POL_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/ADOPS1/HIV1_AMINO/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -31867.45        -31913.67
2     -31866.78        -31913.73
--------------------------------------
TOTAL   -31867.06        -31913.70
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/HIV1_AMINO/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/POL_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/ADOPS1/HIV1_AMINO/POL_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}         3.418357    0.009402    3.230166    3.617533    3.418511   1310.89   1353.43    1.000
r(A<->C){all}   0.079808    0.000017    0.072261    0.088290    0.079717    534.29    599.90    1.000
r(A<->G){all}   0.363347    0.000167    0.338050    0.387642    0.362953    209.67    283.79    1.000
r(A<->T){all}   0.035486    0.000006    0.030684    0.040567    0.035441    908.84    942.87    1.000
r(C<->G){all}   0.036263    0.000017    0.027865    0.043847    0.036092    569.57    616.00    1.000
r(C<->T){all}   0.448445    0.000186    0.421849    0.474013    0.448931    198.90    291.07    1.001
r(G<->T){all}   0.036651    0.000012    0.030062    0.043475    0.036508    666.35    727.15    1.003
pi(A){all}      0.411384    0.000051    0.397827    0.425843    0.411284    530.99    734.49    1.000
pi(C){all}      0.178748    0.000031    0.168612    0.189812    0.178765    505.31    549.76    1.001
pi(G){all}      0.208938    0.000036    0.197626    0.221079    0.208697    591.99    595.90    1.000
pi(T){all}      0.200930    0.000035    0.189085    0.212477    0.200756    688.03    689.13    1.000
alpha{1,2}      0.283481    0.000253    0.252200    0.313110    0.282770   1024.07   1093.12    1.000
alpha{3}        2.212637    0.050530    1.830136    2.690248    2.189349   1202.43   1237.25    1.001
pinvar{all}     0.265349    0.000354    0.231083    0.305367    0.265586   1084.49   1108.16    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	-31214.748226
Model 2: PositiveSelection	-31088.616652
Model 0: one-ratio	-32862.797222
Model 3: discrete	-30879.558554
Model 7: beta	-30961.122093
Model 8: beta&w>1	-30816.421152


Model 0 vs 1	3296.0979920000027

Model 2 vs 1	252.26314799999818

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.BR.10.10BR_SP033.KT427810_)

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

    17 P      0.997**       3.112
    21 T      0.608         2.290
    32 Q      0.939         2.990
    34 R      0.960*        3.034
    36 L      1.000**       3.120
    39 Q      0.781         2.656
    41 L      0.789         2.671
    42 N      1.000**       3.120
    43 F      0.578         2.225
    62 I      0.935         2.981
   106 P      1.000**       3.120
   265 S      1.000**       3.120
   304 S      1.000**       3.119
   349 E      0.925         2.960
   353 K      0.803         2.703
   357 T      0.976*        3.070
   387 Q      0.989*        3.096
   428 T      0.982*        3.080
   476 Q      1.000**       3.120
   499 M      0.843         2.788
   518 A      0.967*        3.049
   519 L      1.000**       3.119
   610 S      0.999**       3.118
   625 Q      1.000**       3.119
   633 S      0.999**       3.118
   696 K      1.000**       3.120
   821 S      0.995**       3.108
   826 N      0.994**       3.107

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: C.BR.10.10BR_SP033.KT427810_)

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

    17 P      0.998**       3.488 +- 0.145
    21 T      0.559         2.393 +- 1.239
    32 Q      0.951*        3.371 +- 0.544
    34 R      0.964*        3.403 +- 0.472
    36 L      1.000**       3.494 +- 0.080
    39 Q      0.723         2.802 +- 1.118
    41 L      0.756         2.883 +- 1.074
    42 N      1.000**       3.494 +- 0.080
    43 F      0.557         2.387 +- 1.240
    62 I      0.912         3.275 +- 0.709
   106 P      1.000**       3.494 +- 0.080
   265 S      1.000**       3.494 +- 0.080
   304 S      1.000**       3.493 +- 0.091
   349 E      0.909         3.268 +- 0.720
   353 K      0.798         2.989 +- 1.004
   357 T      0.979*        3.441 +- 0.368
   387 Q      0.990**       3.469 +- 0.260
   428 T      0.984*        3.454 +- 0.321
   476 Q      1.000**       3.494 +- 0.080
   499 M      0.683         2.701 +- 1.162
   518 A      0.969*        3.416 +- 0.440
   519 L      1.000**       3.493 +- 0.085
   610 S      1.000**       3.493 +- 0.091
   625 Q      1.000**       3.493 +- 0.085
   633 S      0.999**       3.492 +- 0.102
   696 K      1.000**       3.494 +- 0.080
   821 S      0.994**       3.480 +- 0.201
   826 N      0.994**       3.477 +- 0.215


Model 8 vs 7	289.40188200000557

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.BR.10.10BR_SP033.KT427810_)

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

    17 P      1.000**       2.587
    21 T      0.900         2.403
    32 Q      0.984*        2.559
    34 R      0.994**       2.577
    36 L      1.000**       2.588
    39 Q      0.950         2.495
    41 L      0.956*        2.507
    42 N      1.000**       2.588
    43 F      0.846         2.304
    62 I      0.992**       2.573
   106 P      1.000**       2.588
   265 S      1.000**       2.588
   304 S      1.000**       2.588
   349 E      0.991**       2.571
   353 K      0.975*        2.543
   357 T      0.997**       2.582
   387 Q      0.999**       2.586
   428 T      0.998**       2.584
   476 Q      1.000**       2.588
   499 M      0.990**       2.570
   518 A      0.996**       2.580
   519 L      1.000**       2.588
   610 S      1.000**       2.588
   625 Q      1.000**       2.588
   633 S      1.000**       2.588
   696 K      1.000**       2.588
   776 L      0.635         1.906
   821 S      1.000**       2.587
   826 N      1.000**       2.587

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: C.BR.10.10BR_SP033.KT427810_)

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

    17 P      0.999**       2.498 +- 0.054
    21 T      0.896         2.332 +- 0.493
    32 Q      0.980*        2.467 +- 0.227
    34 R      0.989*        2.483 +- 0.163
    36 L      1.000**       2.500 +- 0.001
    39 Q      0.928         2.385 +- 0.412
    41 L      0.944         2.410 +- 0.369
    42 N      1.000**       2.500 +- 0.006
    43 F      0.860         2.273 +- 0.564
    62 I      0.981*        2.470 +- 0.214
   106 P      1.000**       2.500 +- 0.001
   265 S      1.000**       2.500 +- 0.007
   304 S      1.000**       2.500 +- 0.020
   349 E      0.976*        2.463 +- 0.240
   353 K      0.953*        2.426 +- 0.334
   357 T      0.994**       2.490 +- 0.124
   387 Q      0.997**       2.495 +- 0.093
   428 T      0.995**       2.492 +- 0.110
   476 Q      1.000**       2.500 +- 0.003
   499 M      0.971*        2.454 +- 0.266
   518 A      0.992**       2.487 +- 0.142
   519 L      1.000**       2.500 +- 0.012
   610 S      1.000**       2.500 +- 0.026
   625 Q      1.000**       2.500 +- 0.016
   633 S      1.000**       2.499 +- 0.028
   696 K      1.000**       2.500 +- 0.001
   776 L      0.717         2.029 +- 0.753
   821 S      0.998**       2.498 +- 0.063
   826 N      0.998**       2.497 +- 0.064