--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 03 12:50:25 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/Srevisao1/S9_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S9_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/Srevisao1/S9_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -8704.88         -8725.21
2      -8705.71         -8724.37
--------------------------------------
TOTAL    -8705.21         -8724.87
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Srevisao1/S9_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S9_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/Srevisao1/S9_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}         1.556977    0.003577    1.442091    1.668117    1.554608   1315.22   1355.80    1.000
r(A<->C){all}   0.104948    0.000105    0.084777    0.124263    0.104751    942.75    948.58    1.000
r(A<->G){all}   0.294567    0.000298    0.260623    0.327120    0.294445    832.30    879.02    1.001
r(A<->T){all}   0.078047    0.000048    0.064481    0.091334    0.077976    979.07    999.68    1.001
r(C<->G){all}   0.172524    0.000224    0.144664    0.203181    0.171876    965.53    979.77    1.000
r(C<->T){all}   0.275964    0.000277    0.245920    0.310454    0.275420    879.66    947.01    1.001
r(G<->T){all}   0.073951    0.000060    0.057922    0.087927    0.073627    989.36   1067.50    1.000
pi(A){all}      0.306393    0.000123    0.283550    0.326761    0.306268    957.80   1043.87    1.001
pi(C){all}      0.167841    0.000069    0.151204    0.183193    0.167887    799.80    932.23    1.000
pi(G){all}      0.185163    0.000085    0.168269    0.203665    0.185053    651.59    916.80    1.000
pi(T){all}      0.340603    0.000129    0.318609    0.362949    0.340455    976.93   1029.16    1.002
alpha{1,2}      0.881009    0.012791    0.667440    1.099467    0.866690   1147.25   1251.24    1.000
alpha{3}        1.646826    0.123508    1.051852    2.351428    1.596708   1293.01   1323.39    1.000
pinvar{all}     0.032508    0.000698    0.000006    0.084746    0.026109   1125.63   1139.03    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	-5433.53787
Model 2: PositiveSelection	-5400.745793
Model 0: one-ratio	-5562.332691
Model 3: discrete	-5399.793851
Model 7: beta	-5440.093391
Model 8: beta&w>1	-5401.715001


Model 0 vs 1	257.589641999999

Model 2 vs 1	65.58415400000013

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S3_S9_AB539854_MdFBX11)

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

    14 T      0.837         3.163
    20 N      0.999**       3.583
    24 Q      0.992**       3.563
    53 L      0.934         3.412
    58 Y      0.570         2.473
    60 L      0.970*        3.507
    62 L      0.725         2.874
    73 A      0.708         2.828
    85 R      0.515         2.330
   107 V      0.999**       3.581
   109 R      1.000**       3.583
   138 R      0.703         2.816
   155 T      0.743         2.921
   173 S      0.875         3.260
   189 T      1.000**       3.584
   191 A      0.969*        3.503
   219 K      0.681         2.761

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: S3_S9_AB539854_MdFBX11)

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

    14 T      0.780         3.065 +- 1.144
    20 N      0.999**       3.696 +- 0.431
    24 Q      0.990*        3.670 +- 0.503
    53 L      0.914         3.454 +- 0.853
    58 Y      0.501         2.303 +- 1.320
    60 L      0.964*        3.601 +- 0.653
    62 L      0.667         2.766 +- 1.285
    73 A      0.645         2.701 +- 1.296
   107 V      0.999**       3.694 +- 0.438
   109 R      1.000**       3.697 +- 0.429
   138 R      0.647         2.718 +- 1.305
   155 T      0.690         2.835 +- 1.270
   173 S      0.844         3.263 +- 1.044
   189 T      1.000**       3.698 +- 0.427
   191 A      0.960*        3.587 +- 0.671
   219 K      0.618         2.628 +- 1.312


Model 8 vs 7	76.75678000000153

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S3_S9_AB539854_MdFBX11)

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

    14 T      0.935         2.920
    20 N      1.000**       3.058
    24 Q      0.996**       3.050
    53 L      0.969*        2.993
    58 Y      0.796         2.619
    60 L      0.983*        3.023
    62 L      0.863         2.761
    72 T      0.506         1.978
    73 A      0.860         2.755
    85 R      0.702         2.405
   107 V      0.999**       3.057
   109 R      1.000**       3.058
   126 Q      0.562         2.093
   138 R      0.843         2.716
   155 T      0.866         2.766
   170 K      0.734         2.482
   173 S      0.938         2.925
   189 T      1.000**       3.059
   191 A      0.985*        3.027
   219 K      0.839         2.709

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: S3_S9_AB539854_MdFBX11)

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

    14 T      0.870         2.884 +- 0.893
    20 N      1.000**       3.220 +- 0.500
    24 Q      0.994**       3.205 +- 0.529
    53 L      0.949         3.091 +- 0.703
    58 Y      0.662         2.349 +- 1.113
    60 L      0.978*        3.166 +- 0.601
    62 L      0.779         2.653 +- 1.040
    73 A      0.769         2.627 +- 1.049
    85 R      0.593         2.181 +- 1.156
   107 V      0.999**       3.219 +- 0.502
   109 R      1.000**       3.220 +- 0.499
   138 R      0.761         2.610 +- 1.064
   155 T      0.793         2.693 +- 1.028
   170 K      0.601         2.196 +- 1.133
   173 S      0.902         2.972 +- 0.834
   189 T      1.000**       3.221 +- 0.498
   191 A      0.977*        3.163 +- 0.602
   219 K      0.740         2.552 +- 1.077