--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Nov 04 01:34:25 WET 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
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/revmuscle/S7/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S7/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/revmuscle/S7/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -7782.32         -7800.45
2      -7782.68         -7803.97
--------------------------------------
TOTAL    -7782.49         -7803.31
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/revmuscle/S7/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S7/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/revmuscle/S7/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.553233    0.003871    1.437319    1.671137    1.551009   1385.29   1443.15    1.001
r(A<->C){all}   0.115391    0.000133    0.093592    0.137973    0.115214    989.25   1018.81    1.000
r(A<->G){all}   0.302176    0.000330    0.267441    0.336896    0.301816    614.19    752.83    1.000
r(A<->T){all}   0.072014    0.000051    0.058025    0.085796    0.071903   1171.39   1217.05    1.000
r(C<->G){all}   0.157418    0.000226    0.128778    0.187145    0.157070    867.89    868.18    1.001
r(C<->T){all}   0.266934    0.000290    0.231463    0.298372    0.266824    639.01    709.83    1.001
r(G<->T){all}   0.086068    0.000079    0.069042    0.103553    0.085636   1033.08   1096.29    1.000
pi(A){all}      0.299850    0.000118    0.279532    0.321422    0.299853   1003.20   1138.79    1.000
pi(C){all}      0.172852    0.000076    0.156320    0.190205    0.172704    775.36    891.89    1.000
pi(G){all}      0.190047    0.000085    0.171463    0.207282    0.189971   1060.84   1124.68    1.000
pi(T){all}      0.337251    0.000130    0.314160    0.358406    0.337220    997.68   1011.36    1.000
alpha{1,2}      0.865064    0.012832    0.641303    1.075559    0.855112   1044.56   1180.82    1.000
alpha{3}        1.978792    0.208319    1.222132    2.901614    1.909816   1501.00   1501.00    1.000
pinvar{all}     0.030614    0.000634    0.000024    0.080777    0.024200   1365.39   1433.19    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	-5237.548298
Model 2: PositiveSelection	-5201.08564
Model 0: one-ratio	-5367.579411
Model 3: discrete	-5200.812648
Model 7: beta	-5248.360468
Model 8: beta&w>1	-5202.288935


Model 0 vs 1	260.062226

Model 2 vs 1	72.92531599999893

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      0.992**       3.724
    13 R      1.000**       3.744
    17 P      0.956*        3.625
    46 L      0.988*        3.712
    53 E      0.964*        3.648
    66 A      0.585         2.607
    94 R      0.928         3.547
   102 I      1.000**       3.745
   104 T      0.999**       3.744
   150 T      0.569         2.562
   165 E      0.750         3.060
   168 C      0.983*        3.698
   184 T      1.000**       3.745
   186 E      0.991**       3.721

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      0.991**       3.747 +- 0.540
    13 R      0.999**       3.773 +- 0.478
    17 P      0.949         3.624 +- 0.760
    46 L      0.986*        3.735 +- 0.569
    53 E      0.961*        3.666 +- 0.707
    66 A      0.568         2.517 +- 1.357
    94 R      0.916         3.528 +- 0.883
   102 I      1.000**       3.773 +- 0.477
   104 T      0.999**       3.772 +- 0.478
   150 T      0.554         2.486 +- 1.369
   165 E      0.723         2.949 +- 1.259
   168 C      0.981*        3.720 +- 0.603
   184 T      1.000**       3.774 +- 0.475
   186 E      0.990*        3.746 +- 0.546


Model 8 vs 7	92.14306600000054

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      0.998**       3.112
    13 R      1.000**       3.116
    17 P      0.989*        3.091
    46 L      0.997**       3.108
    51 F      0.553         2.098
    53 E      0.987*        3.087
    55 G      0.706         2.443
    66 A      0.863         2.806
    94 R      0.981*        3.073
   102 I      1.000**       3.116
   104 T      1.000**       3.116
   121 Q      0.617         2.227
   133 Q      0.693         2.411
   136 Y      0.567         2.134
   150 T      0.826         2.718
   151 I      0.619         2.258
   165 E      0.941         2.983
   168 C      0.995**       3.104
   184 T      1.000**       3.116
   186 E      0.997**       3.110
   214 K      0.743         2.530

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      0.997**       3.204 +- 0.567
    13 R      1.000**       3.212 +- 0.554
    17 P      0.979*        3.158 +- 0.637
    46 L      0.994**       3.198 +- 0.578
    53 E      0.981*        3.164 +- 0.635
    55 G      0.597         2.145 +- 1.145
    66 A      0.767         2.586 +- 1.060
    94 R      0.965*        3.118 +- 0.690
   102 I      1.000**       3.212 +- 0.554
   104 T      1.000**       3.212 +- 0.554
   121 Q      0.546         2.028 +- 1.187
   133 Q      0.595         2.144 +- 1.159
   150 T      0.733         2.500 +- 1.102
   165 E      0.877         2.878 +- 0.902
   168 C      0.992**       3.191 +- 0.589
   184 T      1.000**       3.212 +- 0.553
   186 E      0.996**       3.202 +- 0.572
   214 K      0.627         2.220 +- 1.137