--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Dec 07 19:27:24 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/402/Spn-PE/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/402/Spn-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/402/Spn-PE/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/402/Spn-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -19698.90        -19713.21
2     -19699.20        -19713.95
--------------------------------------
TOTAL   -19699.04        -19713.65
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/402/Spn-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/402/Spn-PE/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/402/Spn-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.213465    0.001853    1.119721    1.288991    1.212543   1176.47   1218.16    1.000
r(A<->C){all}   0.096282    0.000059    0.081688    0.111408    0.096129   1118.36   1159.12    1.000
r(A<->G){all}   0.230257    0.000147    0.206437    0.253833    0.229974   1186.02   1187.98    1.000
r(A<->T){all}   0.137875    0.000126    0.115429    0.159439    0.137671    805.78    958.82    1.000
r(C<->G){all}   0.068004    0.000029    0.057887    0.078624    0.067981   1096.02   1101.69    1.000
r(C<->T){all}   0.397718    0.000232    0.368205    0.426746    0.397818    825.57    882.29    1.000
r(G<->T){all}   0.069864    0.000049    0.055925    0.082947    0.069802    861.36   1007.17    1.000
pi(A){all}      0.229079    0.000026    0.219368    0.239299    0.229031   1025.66   1050.86    1.000
pi(C){all}      0.305642    0.000031    0.294153    0.316267    0.305671    867.74   1031.60    1.000
pi(G){all}      0.305593    0.000033    0.293962    0.316209    0.305463    884.85    894.37    1.000
pi(T){all}      0.159686    0.000019    0.151348    0.168115    0.159607    881.00    995.50    1.000
alpha{1,2}      0.123166    0.000032    0.113050    0.135277    0.122967   1277.04   1321.00    1.000
alpha{3}        5.037804    0.792318    3.337747    6.672153    4.927351   1400.37   1413.03    1.002
pinvar{all}     0.363499    0.000293    0.330753    0.397261    0.363717   1176.05   1240.49    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	-17152.93027
Model 2: PositiveSelection	-17152.930423
Model 0: one-ratio	-17465.49826
Model 3: discrete	-17125.27371
Model 7: beta	-17137.087421
Model 8: beta&w>1	-17125.369446


Model 0 vs 1	625.1359799999991

Model 2 vs 1	3.060000017285347E-4

Model 8 vs 7	23.43594999999914

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_Spn-PE)

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

    56 V      0.710         0.855
   143 I      0.891         1.013
   149 P      0.993**       1.102
   166 Q      0.976*        1.087
   183 L      0.852         0.979
   188 P      0.939         1.055
   189 S      0.729         0.872
   195 S      0.874         0.998
   273 P      0.535         0.703
   317 R      0.901         1.022
   318 L      0.652         0.805
   356 S      0.927         1.044
   377 T      0.948         1.062
   410 S      0.622         0.779
   415 P      0.829         0.959
   488 S      0.803         0.936
   491 S      0.938         1.054
   495 S      0.914         1.033
   507 A      0.930         1.047
   551 A      0.983*        1.093
   564 Q      0.876         1.000
   565 T      0.943         1.058
   641 S      0.811         0.943
   643 S      0.806         0.939
   645 L      0.728         0.871
   699 L      0.675         0.825
   720 V      0.649         0.802
   805 T      0.641         0.795
   808 S      0.701         0.848
   809 I      0.999**       1.107
   810 Q      0.998**       1.106
   956 T      0.593         0.753
  1013 S      0.597         0.757
  1014 S      0.996**       1.104
  1016 A      0.819         0.950
  1017 P      0.822         0.953
  1030 H      0.594         0.755

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_Spn-PE)

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

    56 V      0.500         1.006 +- 0.514
   143 I      0.769         1.285 +- 0.403
   149 P      0.965*        1.472 +- 0.152
   166 Q      0.923         1.434 +- 0.234
   183 L      0.718         1.228 +- 0.448
   188 P      0.857         1.371 +- 0.323
   189 S      0.626         1.122 +- 0.508
   195 S      0.740         1.256 +- 0.424
   317 R      0.839         1.349 +- 0.355
   318 L      0.523         1.010 +- 0.535
   356 S      0.835         1.350 +- 0.347
   377 T      0.807         1.328 +- 0.360
   415 P      0.641         1.158 +- 0.472
   488 S      0.710         1.215 +- 0.462
   491 S      0.835         1.352 +- 0.343
   495 S      0.751         1.273 +- 0.406
   507 A      0.752         1.276 +- 0.400
   551 A      0.887         1.404 +- 0.274
   564 Q      0.656         1.181 +- 0.456
   565 T      0.855         1.370 +- 0.324
   641 S      0.734         1.238 +- 0.449
   643 S      0.613         1.128 +- 0.484
   645 L      0.520         1.028 +- 0.510
   699 L      0.559         1.047 +- 0.530
   805 T      0.501         0.985 +- 0.540
   808 S      0.580         1.073 +- 0.522
   809 I      0.989*        1.491 +- 0.082
   810 Q      0.974*        1.480 +- 0.125
  1014 S      0.965*        1.472 +- 0.150
  1016 A      0.735         1.241 +- 0.446
  1017 P      0.741         1.247 +- 0.443