--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Oct 31 17:22:04 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/S10_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S10_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/S10_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -8187.19         -8205.96
2      -8186.69         -8207.35
--------------------------------------
TOTAL    -8186.91         -8206.88
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Srevisao/S10_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S10_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/S10_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}         1.500904    0.003399    1.387379    1.612350    1.498621   1501.00   1501.00    1.001
r(A<->C){all}   0.116159    0.000127    0.093586    0.137136    0.115918    797.50    966.84    1.000
r(A<->G){all}   0.304161    0.000312    0.269931    0.337823    0.304084    792.76    866.17    1.000
r(A<->T){all}   0.073605    0.000047    0.060579    0.086789    0.073365   1172.72   1191.28    1.001
r(C<->G){all}   0.153546    0.000208    0.127365    0.183627    0.153141    915.35    921.41    1.000
r(C<->T){all}   0.267489    0.000280    0.233452    0.297932    0.267719    748.52    830.83    1.001
r(G<->T){all}   0.085039    0.000075    0.068658    0.102788    0.084557   1049.55   1083.71    1.000
pi(A){all}      0.298176    0.000111    0.276450    0.318650    0.298086    981.00   1019.93    1.001
pi(C){all}      0.170038    0.000068    0.154566    0.186342    0.170000    806.43    928.97    1.000
pi(G){all}      0.188570    0.000075    0.171619    0.204928    0.188317    826.42    925.19    1.000
pi(T){all}      0.343216    0.000125    0.322118    0.364739    0.343439    927.70    969.61    1.000
alpha{1,2}      0.945389    0.018856    0.705820    1.211655    0.929334   1247.03   1299.01    1.000
alpha{3}        1.734228    0.159330    1.094733    2.534816    1.669443   1214.91   1264.17    1.000
pinvar{all}     0.035114    0.000818    0.000015    0.091155    0.028601   1225.86   1258.89    1.001
------------------------------------------------------------------------------------------------------
* 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	-4760.325842
Model 2: PositiveSelection	-4722.33529
Model 0: one-ratio	-4884.237773
Model 3: discrete	-4722.131359
Model 7: beta	-4771.204726
Model 8: beta&w>1	-4724.825834


Model 0 vs 1	247.82386199999928

Model 2 vs 1	75.98110400000041

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S10_SFBB1)

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

    10 N      0.997**       3.746
    16 R      0.999**       3.752
    20 P      0.999**       3.753
    49 L      0.997**       3.746
    54 F      0.815         3.245
    56 E      0.958*        3.638
    96 R      0.867         3.387
   104 I      0.998**       3.749
   106 T      0.999**       3.751
   123 Q      0.644         2.773
   152 T      0.898         3.472
   167 E      0.754         3.077
   170 C      0.987*        3.717
   186 T      1.000**       3.754
   188 E      0.947         3.609

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: S10_SFBB1)

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

    10 N      0.996**       3.847 +- 0.534
    16 R      0.999**       3.856 +- 0.512
    20 P      0.999**       3.857 +- 0.509
    49 L      0.996**       3.849 +- 0.531
    54 F      0.749         3.090 +- 1.277
    56 E      0.947         3.706 +- 0.807
    96 R      0.818         3.307 +- 1.172
   104 I      0.998**       3.852 +- 0.522
   106 T      0.998**       3.854 +- 0.516
   123 Q      0.585         2.641 +- 1.432
   152 T      0.865         3.456 +- 1.075
   167 E      0.676         2.870 +- 1.347
   170 C      0.983*        3.809 +- 0.623
   186 T      1.000**       3.859 +- 0.504
   188 E      0.930         3.654 +- 0.871


Model 8 vs 7	92.75778399999945

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S10_SFBB1)

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

    10 N      0.999**       3.249
    11 H      0.520         2.092
    16 R      1.000**       3.250
    20 P      1.000**       3.250
    49 L      0.999**       3.248
    54 F      0.941         3.111
    56 E      0.981*        3.205
    58 G      0.524         2.101
    69 A      0.706         2.547
    81 G      0.686         2.494
    93 Q      0.676         2.466
    96 R      0.953*        3.138
   104 I      0.999**       3.249
   106 T      1.000**       3.249
   123 Q      0.798         2.761
   152 T      0.959*        3.154
   167 E      0.918         3.057
   170 C      0.995**       3.238
   186 T      1.000**       3.250
   188 E      0.979*        3.202
   216 K      0.607         2.307

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: S10_SFBB1)

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

    10 N      0.999**       3.158 +- 0.573
    11 H      0.544         1.983 +- 1.115
    16 R      1.000**       3.160 +- 0.570
    20 P      1.000**       3.160 +- 0.569
    49 L      0.999**       3.157 +- 0.574
    54 F      0.912         2.923 +- 0.820
    56 E      0.976*        3.100 +- 0.662
    58 G      0.547         1.993 +- 1.123
    69 A      0.685         2.333 +- 1.092
    81 G      0.671         2.304 +- 1.114
    93 Q      0.664         2.292 +- 1.129
    96 R      0.933         2.980 +- 0.780
   104 I      0.999**       3.158 +- 0.572
   106 T      0.999**       3.159 +- 0.570
   123 Q      0.775         2.580 +- 1.059
   138 Y      0.520         1.923 +- 1.080
   152 T      0.946         3.020 +- 0.750
   167 E      0.881         2.839 +- 0.878
   170 C      0.993**       3.144 +- 0.596
   186 T      1.000**       3.161 +- 0.568
   188 E      0.973*        3.090 +- 0.670
   216 K      0.607         2.135 +- 1.106