--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Nov 08 17:59:26 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/afazermus/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/afazermus/S24_16SFBBs/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/afazermus/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -7156.56         -7175.36
2      -7156.20         -7173.61
--------------------------------------
TOTAL    -7156.36         -7174.83
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/afazermus/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/afazermus/S24_16SFBBs/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/afazermus/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.447229    0.003634    1.335770    1.566210    1.445050   1351.76   1414.83    1.001
r(A<->C){all}   0.120002    0.000147    0.097347    0.144671    0.119452    958.31   1019.37    1.000
r(A<->G){all}   0.301393    0.000377    0.262879    0.338095    0.301383    833.96    869.29    1.000
r(A<->T){all}   0.073112    0.000057    0.058621    0.088271    0.072840   1020.27   1176.74    1.000
r(C<->G){all}   0.155235    0.000242    0.126814    0.187189    0.154745    798.29    911.43    1.000
r(C<->T){all}   0.266778    0.000335    0.231695    0.302710    0.266908    599.68    802.36    1.000
r(G<->T){all}   0.083479    0.000081    0.067219    0.102213    0.083106   1111.91   1177.96    1.001
pi(A){all}      0.294061    0.000116    0.272596    0.315150    0.293560    958.74   1012.23    1.001
pi(C){all}      0.174792    0.000078    0.158384    0.193011    0.174467    984.84   1128.72    1.000
pi(G){all}      0.196583    0.000087    0.178343    0.214911    0.196544    944.00   1109.73    1.003
pi(T){all}      0.334565    0.000127    0.312746    0.356465    0.334628   1035.74   1084.72    1.000
alpha{1,2}      0.789860    0.014972    0.581482    1.035847    0.771309   1223.48   1362.24    1.000
alpha{3}        2.500810    0.495852    1.361102    3.924254    2.362617   1300.59   1331.61    1.000
pinvar{all}     0.050565    0.001313    0.000006    0.119193    0.043952    964.62   1226.54    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	-5182.219563
Model 2: PositiveSelection	-5153.400929
Model 0: one-ratio	-5293.71354
Model 3: discrete	-5153.186482
Model 7: beta	-5190.523449
Model 8: beta&w>1	-5153.987351


Model 0 vs 1	222.98795400000017

Model 2 vs 1	57.637267999998585

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S24_SFBB1)

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

    14 N      0.993**       3.468
    20 R      0.999**       3.483
    24 P      0.973*        3.419
    53 L      0.956*        3.375
    60 E      0.918         3.281
    72 L      0.635         2.578
   101 R      0.829         3.059
   109 I      0.999**       3.482
   111 T      0.999**       3.483
   128 Q      0.882         3.191
   172 E      0.966*        3.401
   174 C      0.853         3.119
   190 T      0.998**       3.481
   192 E      0.809         3.010
   220 K      0.528         2.312
   243 T      0.745         2.851

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: S24_SFBB1)

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

    14 N      0.992**       3.589 +- 0.472
    20 R      0.999**       3.609 +- 0.416
    24 P      0.967*        3.522 +- 0.615
    53 L      0.947         3.469 +- 0.708
    60 E      0.905         3.362 +- 0.857
    72 L      0.577         2.467 +- 1.288
   101 R      0.790         3.041 +- 1.108
   109 I      0.998**       3.607 +- 0.423
   111 T      0.999**       3.609 +- 0.417
   128 Q      0.864         3.253 +- 0.970
   172 E      0.957*        3.493 +- 0.663
   174 C      0.825         3.143 +- 1.051
   190 T      0.998**       3.606 +- 0.426
   192 E      0.771         2.994 +- 1.140
   243 T      0.686         2.752 +- 1.224


Model 8 vs 7	73.07219600000099

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S24_SFBB1)

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

    14 N      0.997**       3.021
    20 R      1.000**       3.025
    24 P      0.990*        3.005
    53 L      0.981*        2.986
    58 F      0.667         2.313
    60 E      0.959*        2.939
    72 L      0.833         2.668
   101 R      0.927         2.870
   109 I      0.999**       3.025
   111 T      1.000**       3.025
   128 Q      0.937         2.891
   140 Q      0.614         2.183
   143 Y      0.596         2.159
   157 T      0.690         2.353
   172 E      0.988*        3.000
   174 C      0.934         2.884
   190 T      0.999**       3.024
   192 E      0.912         2.836
   220 K      0.754         2.496
   237 C      0.620         2.214
   243 T      0.901         2.815

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: S24_SFBB1)

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

    14 N      0.998**       2.826 +- 0.509
    20 R      1.000**       2.831 +- 0.502
    24 P      0.990*        2.809 +- 0.533
    53 L      0.981*        2.790 +- 0.559
    58 F      0.718         2.163 +- 0.870
    60 E      0.961*        2.746 +- 0.615
    72 L      0.840         2.449 +- 0.801
    73 A      0.583         1.883 +- 0.922
    85 G      0.505         1.727 +- 0.957
   101 R      0.926         2.657 +- 0.684
   109 I      0.999**       2.830 +- 0.503
   111 T      1.000**       2.831 +- 0.503
   128 Q      0.940         2.698 +- 0.667
   140 Q      0.669         2.079 +- 0.943
   143 Y      0.674         2.073 +- 0.889
   157 T      0.727         2.202 +- 0.911
   172 E      0.987*        2.802 +- 0.540
   174 C      0.936         2.683 +- 0.669
   190 T      0.999**       2.830 +- 0.505
   192 E      0.913         2.628 +- 0.712
   220 K      0.776         2.303 +- 0.859
   237 C      0.688         2.091 +- 0.867
   243 T      0.896         2.580 +- 0.725