--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Nov 07 11:33:58 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/S2novarevisao/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/S2novarevisao/ClustalW2/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/S2novarevisao/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -8085.47         -8107.94
2      -8085.94         -8105.41
--------------------------------------
TOTAL    -8085.68         -8107.32
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/S2novarevisao/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/S2novarevisao/ClustalW2/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/S2novarevisao/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.444742    0.003042    1.338398    1.552694    1.444209   1316.68   1408.84    1.000
r(A<->C){all}   0.103526    0.000113    0.081898    0.123821    0.103355    904.68   1001.19    1.000
r(A<->G){all}   0.296438    0.000310    0.262285    0.329496    0.296411    732.31    823.04    1.000
r(A<->T){all}   0.075199    0.000053    0.061327    0.090161    0.075138    934.70    983.86    1.000
r(C<->G){all}   0.150343    0.000214    0.120390    0.178529    0.150372    842.35    917.42    1.000
r(C<->T){all}   0.287041    0.000298    0.255438    0.323399    0.286469    767.04    792.46    1.000
r(G<->T){all}   0.087453    0.000080    0.069785    0.104779    0.087248   1044.11   1111.76    1.000
pi(A){all}      0.300048    0.000123    0.279477    0.322492    0.299793    860.17    862.38    1.000
pi(C){all}      0.170234    0.000075    0.152097    0.185967    0.170004    909.42   1049.36    1.000
pi(G){all}      0.190285    0.000078    0.173744    0.208339    0.190258    979.38   1049.38    1.000
pi(T){all}      0.339433    0.000136    0.316789    0.362299    0.339284    886.47    913.36    1.001
alpha{1,2}      0.890622    0.015896    0.652998    1.128527    0.872225   1108.53   1163.72    1.000
alpha{3}        1.829502    0.161855    1.087278    2.584057    1.769971   1166.58   1249.10    1.001
pinvar{all}     0.034348    0.000783    0.000046    0.091076    0.027678   1110.38   1158.99    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	-5305.117167
Model 2: PositiveSelection	-5276.079396
Model 0: one-ratio	-5412.424888
Model 3: discrete	-5274.324693
Model 7: beta	-5310.74118
Model 8: beta&w>1	-5274.669779


Model 0 vs 1	214.61544199999844

Model 2 vs 1	58.075542000000496

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S2_SFBB1)

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

    10 M      0.800         3.039
    27 N      0.985*        3.509
    33 R      0.999**       3.547
    37 P      0.645         2.644
    66 L      0.927         3.364
    73 E      0.997**       3.540
    85 L      0.745         2.899
    86 A      0.541         2.379
   113 R      0.887         3.260
   121 I      0.999**       3.545
   123 T      0.999**       3.547
   140 Q      0.687         2.752
   169 T      0.788         3.009
   187 C      0.544         2.387
   203 T      0.998**       3.545
   205 E      0.961*        3.449

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: S2_SFBB1)

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

    10 M      0.757         3.011 +- 1.194
    27 N      0.980*        3.636 +- 0.577
    33 R      0.999**       3.689 +- 0.452
    37 P      0.586         2.533 +- 1.322
    66 L      0.909         3.438 +- 0.874
    73 E      0.996**       3.682 +- 0.473
    85 L      0.690         2.818 +- 1.262
   113 R      0.855         3.280 +- 1.017
   121 I      0.998**       3.688 +- 0.457
   123 T      0.999**       3.689 +- 0.452
   140 Q      0.644         2.708 +- 1.314
   169 T      0.748         2.991 +- 1.210
   203 T      0.998**       3.687 +- 0.459
   205 E      0.951*        3.556 +- 0.720


Model 8 vs 7	72.1428020000003

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S2_SFBB1)

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

    10 M      0.919         2.789
    27 N      0.995**       2.947
    33 R      1.000**       2.956
    37 P      0.854         2.652
    66 L      0.972*        2.899
    71 F      0.575         2.066
    73 E      0.998**       2.954
    75 G      0.679         2.281
    85 L      0.902         2.754
    86 A      0.791         2.519
   113 R      0.959*        2.873
   121 I      0.999**       2.956
   123 T      1.000**       2.956
   140 Q      0.840         2.618
   152 Q      0.515         1.921
   155 Y      0.588         2.095
   159 A      0.512         1.932
   169 T      0.906         2.760
   184 E      0.643         2.209
   187 C      0.781         2.496
   203 T      0.999**       2.956
   205 E      0.985*        2.927
   255 D      0.674         2.275

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: S2_SFBB1)

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

    10 M      0.890         2.739 +- 0.824
    27 N      0.993**       2.994 +- 0.564
    33 R      1.000**       3.011 +- 0.540
    37 P      0.799         2.506 +- 0.938
    66 L      0.962*        2.919 +- 0.663
    71 F      0.545         1.889 +- 0.990
    73 E      0.998**       3.008 +- 0.545
    75 G      0.627         2.087 +- 1.019
    85 L      0.859         2.658 +- 0.867
    86 A      0.731         2.338 +- 0.991
   113 R      0.941         2.864 +- 0.716
   121 I      0.999**       3.010 +- 0.541
   123 T      1.000**       3.011 +- 0.540
   140 Q      0.807         2.537 +- 0.953
   152 Q      0.507         1.814 +- 1.036
   155 Y      0.554         1.910 +- 0.989
   169 T      0.878         2.711 +- 0.848
   184 E      0.587         1.981 +- 0.995
   187 C      0.726         2.327 +- 1.000
   203 T      0.999**       3.010 +- 0.541
   205 E      0.981*        2.965 +- 0.606
   255 D      0.615         2.051 +- 1.004