--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Oct 31 18:21:44 WET 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=CLUSTALW2
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/Srevisao/S1_18Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S1_18Malus/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/Srevisao/S1_18Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -8479.63         -8499.87
2      -8479.36         -8500.26
--------------------------------------
TOTAL    -8479.49         -8500.09
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Srevisao/S1_18Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S1_18Malus/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/Srevisao/S1_18Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.641477    0.003773    1.523864    1.763089    1.641311   1382.34   1420.51    1.000
r(A<->C){all}   0.116718    0.000121    0.095979    0.139254    0.116461    981.89   1004.16    1.000
r(A<->G){all}   0.297573    0.000314    0.263542    0.331833    0.297515    785.28    887.87    1.001
r(A<->T){all}   0.072904    0.000055    0.058607    0.086703    0.072651    610.02    882.05    1.000
r(C<->G){all}   0.150503    0.000200    0.123780    0.178502    0.149947    881.76   1014.54    1.000
r(C<->T){all}   0.269613    0.000289    0.239373    0.305731    0.268894    782.75    783.82    1.000
r(G<->T){all}   0.092690    0.000078    0.075987    0.110160    0.092362   1005.27   1154.30    1.000
pi(A){all}      0.296435    0.000116    0.274981    0.317367    0.296339    775.83    909.17    1.000
pi(C){all}      0.170889    0.000073    0.153653    0.186329    0.170796    833.37    941.37    1.000
pi(G){all}      0.189965    0.000079    0.171588    0.206267    0.189872    873.65    985.30    1.000
pi(T){all}      0.342710    0.000129    0.320284    0.364795    0.342453   1100.35   1136.58    1.000
alpha{1,2}      0.844618    0.010717    0.670832    1.059716    0.833556   1244.18   1295.08    1.000
alpha{3}        1.934298    0.163856    1.236261    2.732345    1.886747   1258.27   1339.81    1.000
pinvar{all}     0.026634    0.000518    0.000008    0.072645    0.020524   1257.74   1292.78    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	-6252.628628
Model 2: PositiveSelection	-6216.667031
Model 0: one-ratio	-6385.849692
Model 3: discrete	-6215.149793
Model 7: beta	-6260.066885
Model 8: beta&w>1	-6214.282808


Model 0 vs 1	266.4421279999988

Model 2 vs 1	71.92319400000088

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S1_SFBB1)

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

    40 N      1.000**       3.403
    46 R      1.000**       3.403
    50 P      0.996**       3.395
    79 L      0.999**       3.401
    84 F      0.861         3.069
    86 E      0.986*        3.370
    88 G      0.760         2.826
    98 L      0.527         2.266
    99 A      0.891         3.142
   125 R      0.514         2.235
   132 I      0.966*        3.322
   134 T      0.999**       3.400
   151 Q      0.884         3.125
   162 E      0.536         2.289
   195 E      0.601         2.445
   214 T      0.996**       3.395
   216 E      0.944         3.268
   244 K      0.939         3.257

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: S1_SFBB1)

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

    40 N      1.000**       3.531 +- 0.260
    46 R      1.000**       3.531 +- 0.262
    50 P      0.996**       3.522 +- 0.300
    79 L      0.999**       3.529 +- 0.268
    84 F      0.839         3.113 +- 0.954
    86 E      0.986*        3.495 +- 0.395
    88 G      0.728         2.830 +- 1.137
    99 A      0.876         3.210 +- 0.865
   132 I      0.963*        3.438 +- 0.538
   134 T      0.999**       3.528 +- 0.276
   151 Q      0.876         3.216 +- 0.866
   195 E      0.555         2.386 +- 1.252
   214 T      0.996**       3.522 +- 0.300
   216 E      0.938         3.371 +- 0.660
   244 K      0.930         3.351 +- 0.688


Model 8 vs 7	91.5681540000005

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S1_SFBB1)

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

     2 R      0.593         2.063
    23 M      0.530         1.936
    40 N      1.000**       2.918
    46 R      1.000**       2.918
    50 P      0.999**       2.916
    79 L      1.000**       2.918
    84 F      0.956*        2.829
    86 E      0.994**       2.906
    88 G      0.912         2.738
    98 L      0.783         2.472
    99 A      0.963*        2.844
   110 G      0.590         2.055
   125 R      0.766         2.436
   132 I      0.988*        2.893
   134 T      0.999**       2.917
   151 Q      0.949         2.813
   162 E      0.792         2.491
   163 Q      0.526         1.918
   166 Y      0.607         2.112
   180 T      0.532         1.935
   195 E      0.842         2.595
   198 C      0.639         2.169
   214 T      0.998**       2.915
   216 E      0.980*        2.877
   244 K      0.980*        2.878
   267 T      0.691         2.282

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: S1_SFBB1)

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

     2 R      0.626         1.980 +- 0.953
    23 M      0.584         1.883 +- 0.934
    40 N      1.000**       2.841 +- 0.482
    46 R      1.000**       2.840 +- 0.482
    50 P      0.999**       2.838 +- 0.486
    79 L      1.000**       2.840 +- 0.483
    84 F      0.943         2.704 +- 0.637
    86 E      0.994**       2.827 +- 0.504
    88 G      0.894         2.587 +- 0.731
    98 L      0.769         2.291 +- 0.864
    99 A      0.956*        2.736 +- 0.611
   110 G      0.623         1.968 +- 0.950
   125 R      0.756         2.262 +- 0.875
   132 I      0.987*        2.810 +- 0.527
   134 T      0.999**       2.840 +- 0.484
   151 Q      0.946         2.719 +- 0.639
   162 E      0.776         2.305 +- 0.859
   163 Q      0.576         1.876 +- 0.966
   166 Y      0.643         2.002 +- 0.888
   180 T      0.582         1.881 +- 0.947
   195 E      0.816         2.397 +- 0.821
   198 C      0.662         2.051 +- 0.915
   214 T      0.998**       2.837 +- 0.487
   216 E      0.977*        2.787 +- 0.556
   244 K      0.976*        2.784 +- 0.558
   267 T      0.694         2.113 +- 0.889