--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Nov 08 14:39:07 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/afazer/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/afazer/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/afazer/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -7220.69         -7242.17
2      -7221.07         -7241.03
--------------------------------------
TOTAL    -7220.87         -7241.76
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/afazer/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/afazer/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/afazer/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}         1.468552    0.003813    1.352008    1.591112    1.467593   1446.42   1473.71    1.000
r(A<->C){all}   0.122725    0.000150    0.100130    0.147025    0.122558    993.25   1048.60    1.000
r(A<->G){all}   0.301677    0.000343    0.266289    0.339055    0.301739   1024.17   1025.93    1.000
r(A<->T){all}   0.076277    0.000065    0.061683    0.092616    0.075751    978.38    984.05    1.000
r(C<->G){all}   0.147574    0.000240    0.117182    0.178490    0.147331    710.60    769.15    1.003
r(C<->T){all}   0.264095    0.000305    0.231951    0.300486    0.263543    706.23    745.04    1.000
r(G<->T){all}   0.087652    0.000092    0.069672    0.107478    0.087225    916.49   1028.76    1.000
pi(A){all}      0.294814    0.000118    0.274994    0.317496    0.294622    916.51    957.14    1.001
pi(C){all}      0.174971    0.000073    0.159079    0.191901    0.174700    838.09   1035.25    1.000
pi(G){all}      0.197531    0.000091    0.180069    0.216654    0.197468   1062.42   1105.09    1.002
pi(T){all}      0.332683    0.000129    0.310092    0.353711    0.332581    794.04    945.68    1.000
alpha{1,2}      0.751182    0.013573    0.548740    0.985164    0.735424   1161.86   1311.14    1.000
alpha{3}        2.225203    0.357829    1.203322    3.384510    2.128764   1374.50   1407.12    1.000
pinvar{all}     0.049795    0.001356    0.000007    0.121174    0.042494   1311.58   1319.49    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	-5215.795623
Model 2: PositiveSelection	-5188.452727
Model 0: one-ratio	-5337.455602
Model 3: discrete	-5188.061232
Model 7: beta	-5225.672714
Model 8: beta&w>1	-5188.441373


Model 0 vs 1	243.31995800000004

Model 2 vs 1	54.68579200000022

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      0.992**       3.160
    20 R      0.999**       3.175
    24 P      0.972*        3.117
    53 L      0.958*        3.086
    60 E      0.928         3.021
    72 L      0.719         2.565
   101 R      0.752         2.636
   108 I      0.996**       3.168
   110 T      0.998**       3.173
   127 Q      0.856         2.864
   139 Q      0.502         2.093
   156 T      0.580         2.262
   171 E      0.957*        3.084
   174 C      0.884         2.924
   190 T      0.998**       3.173
   192 E      0.839         2.826
   220 K      0.599         2.305
   240 P      0.805         2.753
   241 D      0.958*        3.085
   242 E      0.873         2.901

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      0.990**       3.237 +- 0.529
    20 R      0.999**       3.257 +- 0.488
    24 P      0.966*        3.179 +- 0.626
    53 L      0.951*        3.143 +- 0.679
    60 E      0.919         3.072 +- 0.770
    72 L      0.670         2.458 +- 1.102
   101 R      0.708         2.553 +- 1.081
   108 I      0.995**       3.249 +- 0.506
   110 T      0.998**       3.255 +- 0.494
   127 Q      0.837         2.875 +- 0.941
   156 T      0.542         2.164 +- 1.135
   171 E      0.946         3.128 +- 0.694
   174 C      0.864         2.935 +- 0.892
   190 T      0.998**       3.254 +- 0.494
   192 E      0.809         2.800 +- 0.979
   220 K      0.551         2.175 +- 1.125
   240 P      0.771         2.708 +- 1.026
   241 D      0.948         3.136 +- 0.686
   242 E      0.846         2.887 +- 0.922


Model 8 vs 7	74.46268200000122

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      0.998**       2.733
    20 R      1.000**       2.737
    24 P      0.992**       2.722
    53 L      0.985*        2.710
    58 F      0.759         2.285
    60 E      0.970*        2.682
    62 G      0.516         1.809
    72 L      0.896         2.543
    73 A      0.621         2.014
    85 G      0.506         1.774
   101 R      0.904         2.557
   108 I      0.998**       2.735
   110 T      0.999**       2.736
   127 Q      0.935         2.614
   139 Q      0.712         2.184
   142 Y      0.709         2.190
   156 T      0.780         2.317
   171 E      0.988*        2.715
   174 C      0.956*        2.656
   190 T      0.999**       2.736
   192 E      0.937         2.619
   220 K      0.826         2.410
   237 C      0.760         2.288
   240 P      0.924         2.595
   241 D      0.988*        2.715
   242 E      0.958*        2.660

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

     1 L      0.509         1.643 +- 0.890
    14 N      0.998**       2.517 +- 0.154
    20 R      1.000**       2.519 +- 0.142
    24 P      0.994**       2.509 +- 0.186
    53 L      0.989*        2.501 +- 0.218
    58 F      0.855         2.268 +- 0.594
    60 E      0.978*        2.482 +- 0.281
    62 G      0.662         1.928 +- 0.818
    72 L      0.933         2.403 +- 0.434
    73 A      0.746         2.075 +- 0.750
    85 G      0.629         1.859 +- 0.855
   101 R      0.937         2.410 +- 0.425
   108 I      0.999**       2.517 +- 0.151
   110 T      0.999**       2.518 +- 0.145
   127 Q      0.952*        2.437 +- 0.384
   138 E      0.598         1.817 +- 0.848
   139 Q      0.798         2.163 +- 0.701
   142 Y      0.822         2.211 +- 0.647
   156 T      0.848         2.253 +- 0.626
   171 E      0.992**       2.505 +- 0.203
   174 C      0.970*        2.467 +- 0.316
   190 T      0.999**       2.518 +- 0.146
   192 E      0.957*        2.444 +- 0.366
   220 K      0.888         2.324 +- 0.542
   231 I      0.562         1.753 +- 0.860
   237 C      0.860         2.276 +- 0.583
   240 P      0.949         2.430 +- 0.392
   241 D      0.992**       2.506 +- 0.201
   242 E      0.972*        2.472 +- 0.302