--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Oct 31 19:06:37 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/S24_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S24_17Malus/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/S24_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -7321.50         -7347.97
2      -7321.58         -7340.17
--------------------------------------
TOTAL    -7321.54         -7347.27
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Srevisao/S24_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S24_17Malus/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/S24_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.539856    0.004179    1.413577    1.663098    1.538003   1419.39   1460.20    1.000
r(A<->C){all}   0.119535    0.000141    0.097054    0.143637    0.119242   1036.91   1047.19    1.001
r(A<->G){all}   0.302546    0.000355    0.266413    0.340469    0.302185    770.41    852.92    1.000
r(A<->T){all}   0.075273    0.000059    0.061165    0.091108    0.075001   1197.11   1231.75    1.000
r(C<->G){all}   0.155096    0.000238    0.126628    0.185870    0.154708   1011.64   1044.12    1.000
r(C<->T){all}   0.262896    0.000306    0.227563    0.296297    0.262884    813.12    848.51    1.001
r(G<->T){all}   0.084654    0.000086    0.067474    0.102968    0.084501    934.48   1038.18    1.000
pi(A){all}      0.292303    0.000120    0.272481    0.314436    0.292226    971.69   1114.86    1.000
pi(C){all}      0.175291    0.000076    0.159866    0.194298    0.175144    929.34   1002.94    1.000
pi(G){all}      0.196941    0.000092    0.178868    0.214956    0.196643    805.02    926.84    1.000
pi(T){all}      0.335465    0.000130    0.314464    0.358724    0.335305   1106.01   1117.18    1.000
alpha{1,2}      0.731149    0.010507    0.548909    0.935565    0.717856   1218.11   1271.50    1.000
alpha{3}        2.301397    0.358154    1.293062    3.384344    2.209746   1371.55   1419.94    1.000
pinvar{all}     0.043361    0.001042    0.000004    0.103679    0.036569   1229.64   1296.22    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	-3432.591325
Model 2: PositiveSelection	-3412.089337
Model 0: one-ratio	-3512.847386
Model 3: discrete	-3412.070558
Model 7: beta	-3436.013498
Model 8: beta&w>1	-3412.652165


Model 0 vs 1	160.5121220000001

Model 2 vs 1	41.003975999999966

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S24_SFBB1)

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

     2 E      0.911         3.792
    43 R      0.631         2.932
    50 I      0.999**       4.060
    52 T      0.999**       4.061
    69 Q      0.609         2.864
    84 Y      0.505         2.548
   113 E      0.967*        3.963
   116 C      0.961*        3.943
   132 T      1.000**       4.062
   134 E      0.891         3.728

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: S24_SFBB1)

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

     2 E      0.892         3.922 +- 1.238
    43 R      0.548         2.687 +- 1.606
    50 I      0.999**       4.280 +- 0.764
    52 T      0.999**       4.282 +- 0.761
    69 Q      0.557         2.774 +- 1.667
   113 E      0.946         4.083 +- 1.025
   116 C      0.949         4.112 +- 1.025
   132 T      1.000**       4.283 +- 0.760
   134 E      0.848         3.739 +- 1.337


Model 8 vs 7	46.72266599999966

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S24_SFBB1)

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

     2 E      0.943         3.406
    43 R      0.791         3.006
    50 I      0.999**       3.554
    52 T      1.000**       3.555
    69 Q      0.729         2.837
    81 Q      0.509         2.246
    84 Y      0.710         2.794
   113 E      0.984*        3.513
   116 C      0.976*        3.493
   132 T      1.000**       3.555
   134 E      0.940         3.398

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: S24_SFBB1)

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

     2 E      0.929         3.536 +- 1.022
    43 R      0.699         2.789 +- 1.364
    50 I      0.999**       3.746 +- 0.743
    52 T      1.000**       3.746 +- 0.742
    69 Q      0.668         2.735 +- 1.434
    84 Y      0.607         2.503 +- 1.387
   113 E      0.974*        3.663 +- 0.852
   116 C      0.969*        3.655 +- 0.878
   132 T      1.000**       3.746 +- 0.741
   134 E      0.913         3.474 +- 1.057