--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 03 11:19:58 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/Srevisao1/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S5_16Malus/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/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -7545.50         -7563.99
2      -7544.86         -7568.18
--------------------------------------
TOTAL    -7545.13         -7567.51
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Srevisao1/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S5_16Malus/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/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.469208    0.003508    1.350087    1.578394    1.468084   1498.65   1499.82    1.000
r(A<->C){all}   0.107501    0.000134    0.084432    0.129230    0.106798   1008.14   1015.87    1.000
r(A<->G){all}   0.320348    0.000335    0.284494    0.356604    0.319870    903.62    940.71    1.001
r(A<->T){all}   0.083122    0.000065    0.068407    0.099767    0.082883   1081.42   1179.92    1.000
r(C<->G){all}   0.143599    0.000213    0.115425    0.172392    0.143039   1013.84   1015.05    1.000
r(C<->T){all}   0.262472    0.000285    0.228995    0.294284    0.262325    772.45    914.42    1.000
r(G<->T){all}   0.082959    0.000082    0.066133    0.102474    0.082508    960.09    971.38    1.000
pi(A){all}      0.292989    0.000114    0.272272    0.313511    0.292875    947.09    982.35    1.001
pi(C){all}      0.174676    0.000076    0.158774    0.192560    0.174447   1044.93   1074.65    1.000
pi(G){all}      0.193692    0.000082    0.175236    0.210526    0.193632    785.24    825.35    1.000
pi(T){all}      0.338643    0.000135    0.315395    0.360700    0.338227    840.18    941.82    1.002
alpha{1,2}      1.007668    0.037610    0.685566    1.371147    0.978509   1063.82   1103.30    1.000
alpha{3}        1.525199    0.159300    0.912001    2.316682    1.448358   1127.18   1285.60    1.000
pinvar{all}     0.060690    0.001948    0.000012    0.146064    0.051403   1026.57   1096.92    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	-3660.050783
Model 2: PositiveSelection	-3636.130604
Model 0: one-ratio	-3740.088089
Model 3: discrete	-3633.973648
Model 7: beta	-3659.557345
Model 8: beta&w>1	-3633.174241


Model 0 vs 1	160.07461199999943

Model 2 vs 1	47.84035800000038

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S5_SFBB1)

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

     8 L      0.560         2.662
    35 R      0.872         3.590
    43 I      0.999**       3.967
    45 T      0.999**       3.968
    62 Q      0.830         3.464
    74 Q      0.542         2.611
    77 Y      0.677         3.011
   106 E      0.997**       3.962
   109 C      0.952*        3.827
   125 T      1.000**       3.970
   127 E      0.964*        3.864
   155 K      0.683         3.028
   175 P      0.734         3.180

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: S5_SFBB1)

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

    35 R      0.823         3.567 +- 1.326
    43 I      0.999**       4.175 +- 0.691
    45 T      0.999**       4.177 +- 0.687
    62 Q      0.793         3.497 +- 1.404
    77 Y      0.602         2.824 +- 1.558
   106 E      0.996**       4.167 +- 0.707
   109 C      0.936         3.966 +- 1.010
   125 T      1.000**       4.179 +- 0.683
   127 E      0.953*        4.023 +- 0.940
   155 K      0.606         2.841 +- 1.559
   175 P      0.674         3.084 +- 1.541


Model 8 vs 7	52.766208000000006

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S5_SFBB1)

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

     8 L      0.706         2.673
    20 G      0.589         2.374
    35 R      0.917         3.197
    43 I      0.999**       3.401
    45 T      0.999**       3.402
    62 Q      0.878         3.097
    74 Q      0.666         2.566
    77 Y      0.794         2.892
   106 E      0.997**       3.396
   109 C      0.968*        3.324
   125 T      1.000**       3.403
   127 E      0.975*        3.342
   155 K      0.792         2.886
   175 P      0.829         2.976

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: S5_SFBB1)

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

     8 L      0.621         2.390 +- 1.262
    20 G      0.519         2.114 +- 1.268
    35 R      0.879         3.145 +- 1.036
    43 I      0.999**       3.499 +- 0.680
    45 T      0.999**       3.500 +- 0.678
    62 Q      0.845         3.064 +- 1.120
    74 Q      0.600         2.354 +- 1.303
    77 Y      0.721         2.680 +- 1.229
   106 E      0.997**       3.492 +- 0.690
   109 C      0.958*        3.381 +- 0.840
   125 T      1.000**       3.501 +- 0.676
   127 E      0.968*        3.411 +- 0.806
   155 K      0.719         2.677 +- 1.239
   175 P      0.775         2.851 +- 1.206