--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Dec 02 18:36:29 WET 2016
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=/opt/ADOPS/90/CG1718-PD/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/90/CG1718-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/90/CG1718-PD/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/ADOPS/90/CG1718-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -18161.96        -18176.60
2     -18161.30        -18176.42
--------------------------------------
TOTAL   -18161.57        -18176.52
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/90/CG1718-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/90/CG1718-PD/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/ADOPS/90/CG1718-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.105362    0.001597    1.028892    1.182118    1.103649   1286.95   1377.15    1.000
r(A<->C){all}   0.111609    0.000080    0.094142    0.129128    0.111386   1047.79   1052.63    1.000
r(A<->G){all}   0.254902    0.000182    0.228640    0.282646    0.254589    742.20    928.14    1.001
r(A<->T){all}   0.089965    0.000092    0.072404    0.109372    0.089690    881.03    975.80    1.001
r(C<->G){all}   0.079673    0.000041    0.067718    0.092461    0.079664    955.26   1036.83    1.000
r(C<->T){all}   0.406589    0.000248    0.376943    0.437371    0.406353    746.20    888.19    1.001
r(G<->T){all}   0.057263    0.000039    0.044702    0.069158    0.056885    971.84   1069.45    1.000
pi(A){all}      0.223614    0.000031    0.212719    0.234222    0.223460    801.08    927.54    1.000
pi(C){all}      0.269437    0.000030    0.258650    0.279810    0.269381    813.64    999.94    1.000
pi(G){all}      0.280391    0.000034    0.269085    0.291775    0.280460    939.96    991.62    1.000
pi(T){all}      0.226557    0.000028    0.216322    0.236725    0.226404    712.19    904.94    1.000
alpha{1,2}      0.144805    0.000052    0.131253    0.159132    0.144664   1037.81   1211.72    1.000
alpha{3}        6.685932    1.481960    4.471328    9.107367    6.581140   1286.48   1312.75    1.001
pinvar{all}     0.288846    0.000379    0.251373    0.324688    0.289402   1119.80   1291.54    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	-16630.240949
Model 2: PositiveSelection	-16626.692168
Model 0: one-ratio	-16973.926608
Model 3: discrete	-16610.67111
Model 7: beta	-16627.595909
Model 8: beta&w>1	-16611.751472


Model 0 vs 1	687.371318000005

Model 2 vs 1	7.097561999995378

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_CG1718-PD)

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

   944 Q      0.949         6.099
   946 Y      0.908         5.876

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: D_melanogaster_CG1718-PD)

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

    57 R      0.525         1.248 +- 0.289
    58 Y      0.599         1.298 +- 0.249
    60 N      0.581         1.289 +- 0.249
    61 E      0.577         1.288 +- 0.248
    63 N      0.522         1.259 +- 0.256
    72 K      0.805         1.402 +- 0.198
    77 S      0.603         1.295 +- 0.264
   106 N      0.572         1.284 +- 0.253
   107 K      0.842         1.421 +- 0.182
   124 K      0.670         1.335 +- 0.235
   142 N      0.640         1.320 +- 0.240
   144 P      0.656         1.328 +- 0.238
   190 D      0.625         1.312 +- 0.242
   221 E      0.550         1.274 +- 0.253
   319 S      0.553         1.275 +- 0.253
   321 D      0.582         1.290 +- 0.250
   944 Q      0.915         1.457 +- 0.140
   945 G      0.549         1.275 +- 0.249
   946 Y      0.888         1.444 +- 0.158
   954 D      0.531         1.264 +- 0.255
   957 R      0.566         1.274 +- 0.274
  1002 K      0.659         1.330 +- 0.237
  1028 D      0.563         1.281 +- 0.249
  1032 S      0.719         1.359 +- 0.225
  1033 S      0.598         1.298 +- 0.247
  1315 T      0.582         1.290 +- 0.248


Model 8 vs 7	31.688873999999487

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_CG1718-PD)

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

    57 R      0.781         0.955
    58 Y      0.918         1.082
    60 N      0.929         1.092
    61 E      0.951*        1.112
    63 N      0.875         1.043
    72 K      0.999**       1.156
    76 F      0.869         1.037
    77 S      0.880         1.047
    82 I      0.747         0.925
    93 K      0.761         0.938
    97 E      0.819         0.991
   105 K      0.804         0.978
   106 N      0.898         1.064
   107 K      1.000**       1.157
   119 L      0.614         0.802
   124 K      0.987*        1.145
   142 N      0.970*        1.129
   144 P      0.981*        1.139
   190 D      0.970*        1.129
   218 K      0.523         0.717
   221 E      0.905         1.070
   223 D      0.717         0.897
   226 N      0.820         0.992
   319 S      0.906         1.071
   321 D      0.925         1.088
   342 V      0.569         0.760
   452 I      0.822         0.994
   913 K      0.556         0.748
   942 N      0.677         0.860
   944 Q      1.000**       1.157
   945 G      0.951*        1.113
   946 Y      1.000**       1.157
   954 D      0.885         1.051
   957 R      0.844         1.013
   970 T      0.877         1.044
   971 Q      0.803         0.977
   972 G      0.769         0.945
   979 D      0.512         0.708
   999 T      0.679         0.863
  1002 K      0.990*        1.148
  1028 D      0.955*        1.116
  1031 F      0.716         0.897
  1032 S      0.978*        1.137
  1033 S      0.945         1.106
  1035 K      0.757         0.934
  1307 I      0.600         0.784
  1315 T      0.946         1.108
  1318 Q      0.705         0.886
  1590 Y      0.710         0.891

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: D_melanogaster_CG1718-PD)

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

    57 R      0.656         1.155 +- 0.494
    58 Y      0.809         1.323 +- 0.374
    60 N      0.802         1.319 +- 0.375
    61 E      0.813         1.333 +- 0.358
    63 N      0.708         1.225 +- 0.442
    72 K      0.977*        1.482 +- 0.117
    76 F      0.679         1.197 +- 0.455
    77 S      0.796         1.304 +- 0.400
    93 K      0.518         1.029 +- 0.508
    97 E      0.626         1.139 +- 0.483
   105 K      0.589         1.104 +- 0.490
   106 N      0.773         1.288 +- 0.404
   107 K      0.985*        1.489 +- 0.092
   124 K      0.913         1.427 +- 0.242
   142 N      0.878         1.393 +- 0.293
   144 P      0.900         1.414 +- 0.263
   190 D      0.867         1.384 +- 0.304
   221 E      0.758         1.275 +- 0.410
   223 D      0.561         1.052 +- 0.527
   226 N      0.616         1.130 +- 0.485
   319 S      0.763         1.280 +- 0.407
   321 D      0.801         1.317 +- 0.377
   452 I      0.624         1.138 +- 0.482
   944 Q      0.995**       1.497 +- 0.050
   945 G      0.792         1.314 +- 0.372
   946 Y      0.992**       1.494 +- 0.068
   954 D      0.725         1.242 +- 0.433
   957 R      0.738         1.244 +- 0.445
   970 T      0.664         1.185 +- 0.457
   971 Q      0.616         1.127 +- 0.489
   972 G      0.526         1.037 +- 0.506
  1002 K      0.911         1.425 +- 0.244
  1028 D      0.807         1.329 +- 0.360
  1031 F      0.529         1.031 +- 0.516
  1032 S      0.929         1.438 +- 0.228
  1033 S      0.829         1.346 +- 0.349
  1035 K      0.501         1.012 +- 0.509
  1307 I      0.513         0.950 +- 0.590
  1315 T      0.818         1.336 +- 0.357
  1318 Q      0.568         1.056 +- 0.529
  1590 Y      0.546         1.037 +- 0.529