--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 03 12:07:39 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/S7_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S7_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/S7_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -7915.22         -7935.70
2      -7915.01         -7933.70
--------------------------------------
TOTAL    -7915.11         -7935.13
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Srevisao1/S7_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S7_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/S7_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}         1.589672    0.004085    1.456892    1.705429    1.587433   1043.54   1272.27    1.000
r(A<->C){all}   0.117515    0.000130    0.096695    0.141061    0.117128    988.54   1065.17    1.000
r(A<->G){all}   0.303197    0.000325    0.269052    0.338053    0.302873    817.32    896.92    1.001
r(A<->T){all}   0.074985    0.000054    0.060870    0.089325    0.074626    812.45   1005.82    1.000
r(C<->G){all}   0.154773    0.000220    0.126708    0.184607    0.154099    639.35    895.64    1.000
r(C<->T){all}   0.261598    0.000287    0.226693    0.292429    0.260863    807.44    934.66    1.001
r(G<->T){all}   0.087932    0.000083    0.070630    0.105576    0.087740   1040.30   1081.95    1.000
pi(A){all}      0.300437    0.000122    0.280056    0.322574    0.300170   1009.77   1072.74    1.000
pi(C){all}      0.171786    0.000076    0.155331    0.188508    0.171553    823.94    959.45    1.000
pi(G){all}      0.190639    0.000084    0.172114    0.207917    0.190579   1008.26   1052.83    1.000
pi(T){all}      0.337137    0.000135    0.315026    0.360121    0.337238    938.56   1017.40    1.000
alpha{1,2}      0.839014    0.011414    0.645197    1.044926    0.828820   1369.33   1384.42    1.000
alpha{3}        1.893832    0.173251    1.191888    2.820625    1.837140   1252.48   1376.74    1.000
pinvar{all}     0.031848    0.000651    0.000000    0.081065    0.025492   1414.25   1436.11    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	-5328.244827
Model 2: PositiveSelection	-5288.218606
Model 0: one-ratio	-5473.429714
Model 3: discrete	-5287.815107
Model 7: beta	-5340.138853
Model 8: beta&w>1	-5289.777434


Model 0 vs 1	290.36977399999887

Model 2 vs 1	80.05244200000016

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S7_SFBB1)

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

     7 N      0.997**       3.596
    13 R      0.999**       3.603
    17 P      0.995**       3.591
    46 L      0.988*        3.573
    53 E      0.934         3.433
    66 A      0.650         2.692
    93 S      0.999**       3.601
    94 R      0.925         3.409
   100 I      0.999**       3.602
   102 T      0.999**       3.603
   131 Q      0.525         2.367
   148 T      0.600         2.564
   163 E      0.794         3.069
   166 C      0.965*        3.513
   182 T      1.000**       3.604
   184 E      0.992**       3.583
   232 P      0.662         2.724

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: S7_SFBB1)

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

     7 N      0.996**       3.657 +- 0.432
    13 R      0.999**       3.668 +- 0.402
    17 P      0.994**       3.653 +- 0.447
    46 L      0.985*        3.629 +- 0.508
    53 E      0.922         3.458 +- 0.810
    66 A      0.598         2.554 +- 1.300
    93 S      0.999**       3.666 +- 0.409
    94 R      0.904         3.402 +- 0.862
   100 I      0.999**       3.666 +- 0.407
   102 T      0.999**       3.667 +- 0.403
   148 T      0.552         2.436 +- 1.318
   163 E      0.745         2.948 +- 1.179
   166 C      0.957*        3.552 +- 0.664
   182 T      1.000**       3.669 +- 0.398
   184 E      0.990*        3.642 +- 0.476
   232 P      0.615         2.606 +- 1.301


Model 8 vs 7	100.7228380000015

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S7_SFBB1)

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

     7 N      0.999**       3.050
    13 R      1.000**       3.051
    17 P      0.999**       3.048
    46 L      0.996**       3.044
    51 F      0.815         2.645
    53 E      0.974*        2.995
    55 G      0.730         2.452
    66 A      0.881         2.790
    93 S      1.000**       3.051
    94 R      0.980*        3.007
   100 I      1.000**       3.051
   102 T      1.000**       3.051
   119 Q      0.634         2.225
   131 Q      0.776         2.551
   134 Y      0.545         2.048
   148 T      0.831         2.676
   149 I      0.617         2.212
   163 E      0.947         2.937
   166 C      0.989*        3.028
   182 T      1.000**       3.051
   184 E      0.997**       3.046
   212 K      0.747         2.491
   232 P      0.871         2.766

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: S7_SFBB1)

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

     7 N      0.999**       2.852 +- 0.502
    13 R      1.000**       2.854 +- 0.500
    17 P      0.998**       2.851 +- 0.505
    46 L      0.996**       2.845 +- 0.513
    51 F      0.807         2.381 +- 0.835
    53 E      0.971*        2.790 +- 0.590
    55 G      0.748         2.258 +- 0.905
    65 L      0.567         1.855 +- 0.942
    66 A      0.869         2.537 +- 0.782
    78 G      0.574         1.873 +- 0.976
    93 S      1.000**       2.854 +- 0.500
    94 R      0.975*        2.794 +- 0.577
   100 I      1.000**       2.854 +- 0.500
   102 T      1.000**       2.854 +- 0.500
   119 Q      0.672         2.104 +- 0.986
   131 Q      0.783         2.343 +- 0.889
   134 Y      0.635         1.997 +- 0.915
   148 T      0.828         2.444 +- 0.843
   149 I      0.677         2.075 +- 0.882
   163 E      0.932         2.688 +- 0.670
   166 C      0.987*        2.825 +- 0.541
   182 T      1.000**       2.855 +- 0.499
   184 E      0.997**       2.848 +- 0.510
   212 K      0.760         2.280 +- 0.892
   232 P      0.863         2.528 +- 0.797