--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Mar 22 23:31:10 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_3/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/HIV1_AMINO/POL_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/POL_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/ADOPS1/HIV1_AMINO/POL_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -32106.91        -32146.16
2     -32106.99        -32148.28
--------------------------------------
TOTAL   -32106.95        -32147.70
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/HIV1_AMINO/POL_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/POL_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/ADOPS1/HIV1_AMINO/POL_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}         4.448104    0.021276    4.166619    4.726056    4.446546    816.80    834.10    1.001
r(A<->C){all}   0.070767    0.000014    0.063599    0.078045    0.070740    633.73    738.14    1.000
r(A<->G){all}   0.350947    0.000171    0.324406    0.375922    0.351052    254.32    292.62    1.000
r(A<->T){all}   0.034174    0.000006    0.029456    0.038894    0.034063    761.60    763.88    1.001
r(C<->G){all}   0.040513    0.000016    0.033246    0.048731    0.040425    744.19    764.41    1.000
r(C<->T){all}   0.462283    0.000195    0.435933    0.490261    0.462198    231.93    297.69    1.000
r(G<->T){all}   0.041315    0.000013    0.034660    0.048608    0.041090    622.91    808.93    1.000
pi(A){all}      0.415231    0.000047    0.402419    0.428760    0.415142    535.44    643.14    1.000
pi(C){all}      0.177465    0.000028    0.167570    0.188269    0.177398    496.11    535.82    1.000
pi(G){all}      0.201887    0.000030    0.191497    0.212529    0.201919    403.84    555.80    1.000
pi(T){all}      0.205417    0.000032    0.194749    0.216436    0.205525    508.89    574.59    1.000
alpha{1,2}      0.284342    0.000222    0.255404    0.313168    0.283921    918.54   1101.50    1.000
alpha{3}        1.977800    0.034052    1.627663    2.354594    1.964390   1104.46   1254.81    1.000
pinvar{all}     0.229181    0.000299    0.192918    0.260842    0.229314    908.28   1175.20    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	-30976.13334
Model 2: PositiveSelection	-30890.799689
Model 0: one-ratio	-32515.656112
Model 3: discrete	-30727.775711
Model 7: beta	-30800.989058
Model 8: beta&w>1	-30689.158983


Model 0 vs 1	3079.0455440000005

Model 2 vs 1	170.66730200000165

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.KR.99.99HYH2.JQ316129_)

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

    30 Q      0.880         2.956
    36 F      0.969*        3.155
    37 S      0.937         3.084
    48 L      0.975*        3.168
   101 T      1.000**       3.223
   260 D      1.000**       3.223
   310 K      0.923         3.053
   348 R      1.000**       3.223
   382 L      0.516         2.148
   423 T      0.990**       3.202
   471 Q      0.864         2.920
   513 A      0.958*        3.130
   605 P      0.995**       3.213
   620 H      0.964*        3.142
   691 A      1.000**       3.223
   816 G      0.743         2.652
   821 N      1.000**       3.223

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.KR.99.99HYH2.JQ316129_)

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

    20 T      0.628         2.415 +- 1.141
    30 Q      0.937         3.155 +- 0.680
    36 F      0.984*        3.264 +- 0.490
    37 S      0.963*        3.212 +- 0.586
    48 L      0.988*        3.275 +- 0.469
   101 T      1.000**       3.301 +- 0.399
   260 D      1.000**       3.301 +- 0.400
   310 K      0.947         3.170 +- 0.649
   348 R      1.000**       3.301 +- 0.399
   382 L      0.664         2.497 +- 1.121
   423 T      0.995**       3.290 +- 0.429
   471 Q      0.918         3.105 +- 0.738
   513 A      0.979*        3.252 +- 0.516
   605 P      0.998**       3.296 +- 0.414
   620 H      0.980*        3.254 +- 0.510
   691 A      1.000**       3.301 +- 0.399
   816 G      0.825         2.875 +- 0.944
   821 N      1.000**       3.301 +- 0.399


Model 8 vs 7	223.66014999999607

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.KR.99.99HYH2.JQ316129_)

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

     9 P      0.559         1.529
    20 T      0.960*        2.156
    30 Q      0.993**       2.208
    34 Q      0.921         2.096
    36 F      0.999**       2.218
    37 S      0.999**       2.218
    38 F      0.854         1.990
    48 L      0.996**       2.213
   101 T      1.000**       2.219
   260 D      1.000**       2.219
   310 K      1.000**       2.219
   348 R      1.000**       2.219
   382 L      0.974*        2.178
   414 R      0.968*        2.170
   423 T      1.000**       2.219
   471 Q      0.997**       2.214
   513 A      0.998**       2.217
   514 T      0.893         2.051
   516 G      0.566         1.539
   572 V      0.997**       2.214
   589 L      0.899         2.061
   605 P      1.000**       2.219
   620 H      0.999**       2.218
   628 L      0.569         1.544
   661 Q      0.572         1.547
   691 A      1.000**       2.219
   769 V      0.931         2.112
   816 G      0.996**       2.213
   821 N      1.000**       2.219

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.KR.99.99HYH2.JQ316129_)

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

    20 T      0.888         2.319 +- 0.511
    30 Q      0.978*        2.465 +- 0.235
    34 Q      0.721         2.052 +- 0.723
    36 F      0.994**       2.490 +- 0.125
    37 S      0.989*        2.483 +- 0.163
    38 F      0.720         2.044 +- 0.735
    48 L      0.992**       2.487 +- 0.146
   101 T      1.000**       2.500 +- 0.001
   260 D      1.000**       2.500 +- 0.013
   310 K      0.989*        2.483 +- 0.162
   348 R      1.000**       2.500 +- 0.006
   382 L      0.896         2.332 +- 0.491
   414 R      0.805         2.188 +- 0.634
   423 T      0.998**       2.497 +- 0.071
   471 Q      0.973*        2.457 +- 0.257
   513 A      0.993**       2.488 +- 0.136
   572 V      0.874         2.301 +- 0.524
   589 L      0.554         1.785 +- 0.798
   605 P      0.999**       2.498 +- 0.057
   620 H      0.993**       2.488 +- 0.135
   691 A      1.000**       2.500 +- 0.002
   769 V      0.755         2.106 +- 0.693
   816 G      0.962*        2.439 +- 0.305
   821 N      1.000**       2.500 +- 0.004