--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Apr 16 13:52:01 WEST 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=
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/HIV1_AM/batch2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AM/batch2/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_AM/batch2/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -11370.18        -11414.43
2     -11370.19        -11414.59
--------------------------------------
TOTAL   -11370.18        -11414.51
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/HIV1_AM/batch2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AM/batch2/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_AM/batch2/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         6.788471    0.094836    6.155887    7.368659    6.786524    676.34    821.55    1.000
r(A<->C){all}   0.107162    0.000070    0.091007    0.123545    0.106991    668.05    705.78    1.000
r(A<->G){all}   0.310907    0.000370    0.272288    0.347417    0.311561    319.83    408.85    1.000
r(A<->T){all}   0.093456    0.000072    0.077172    0.109695    0.093146    643.67    691.79    1.000
r(C<->G){all}   0.063819    0.000057    0.048840    0.078160    0.063342    729.08    757.80    1.000
r(C<->T){all}   0.329600    0.000420    0.291438    0.371954    0.328484    319.37    437.92    1.000
r(G<->T){all}   0.095055    0.000090    0.077447    0.114257    0.094688    723.23    753.85    1.003
pi(A){all}      0.353395    0.000149    0.330538    0.377653    0.353542    569.64    579.71    1.000
pi(C){all}      0.221142    0.000115    0.199015    0.241226    0.221232    588.32    613.62    1.001
pi(G){all}      0.241231    0.000118    0.220986    0.262965    0.241322    647.19    677.17    1.001
pi(T){all}      0.184232    0.000091    0.166427    0.203442    0.184077    588.54    626.01    1.000
alpha{1,2}      0.461161    0.001704    0.385411    0.542779    0.458314   1030.56   1175.59    1.000
alpha{3}        2.270255    0.118429    1.625646    2.950286    2.248987   1254.35   1307.79    1.000
pinvar{all}     0.068206    0.000523    0.025267    0.113319    0.066902    858.76   1048.13    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	-8780.802191
Model 2: PositiveSelection	-8725.666742
Model 0: one-ratio	-9263.633309
Model 3: discrete	-8701.755116
Model 7: beta	-8732.755948
Model 8: beta&w>1	-8686.864626


Model 0 vs 1	965.6622360000001

Model 2 vs 1	110.27089800000249

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.ZA.08.as03_0513.KM262928_)

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

     8 P      0.820         2.566
     9 N      0.997**       2.904
   107 V      1.000**       2.910
   125 R      0.999**       2.908
   131 C      0.997**       2.904
   149 M      1.000**       2.910
   155 S      1.000**       2.910
   161 L      0.989*        2.889
   165 K      1.000**       2.910

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.ZA.08.as03_0513.KM262928_)

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

     8 P      0.789         2.363 +- 0.798
     9 N      0.996**       2.784 +- 0.469
   107 V      1.000**       2.792 +- 0.455
   125 R      0.998**       2.788 +- 0.460
   131 C      0.995**       2.782 +- 0.470
   149 M      1.000**       2.791 +- 0.455
   155 S      1.000**       2.792 +- 0.455
   161 L      0.975*        2.735 +- 0.521
   165 K      1.000**       2.792 +- 0.455


Model 8 vs 7	91.78264399999898

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.ZA.08.as03_0513.KM262928_)

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

     8 P      0.849         2.147
     9 N      0.995**       2.360
   107 V      1.000**       2.367
   125 R      0.998**       2.364
   131 C      0.995**       2.360
   149 M      1.000**       2.366
   155 S      1.000**       2.367
   161 L      0.981*        2.340
   165 K      1.000**       2.367

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.ZA.08.as03_0513.KM262928_)

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

     8 P      0.777         2.148 +- 0.658
     9 N      0.993**       2.488 +- 0.134
   107 V      1.000**       2.500 +- 0.011
   125 R      0.996**       2.494 +- 0.098
   131 C      0.992**       2.488 +- 0.138
   149 M      0.999**       2.499 +- 0.042
   155 S      1.000**       2.500 +- 0.016
   161 L      0.963*        2.442 +- 0.296
   165 K      1.000**       2.500 +- 0.006