--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Dec 07 13:57:05 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/408/Sudx-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/408/Sudx-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/408/Sudx-PA/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/408/Sudx-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -10162.07        -10179.24
2     -10162.69        -10181.17
--------------------------------------
TOTAL   -10162.33        -10180.61
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/408/Sudx-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/408/Sudx-PA/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/408/Sudx-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.282424    0.004054    1.155376    1.401699    1.278382   1238.64   1369.82    1.000
r(A<->C){all}   0.093619    0.000099    0.073675    0.111975    0.093537    864.36    941.50    1.001
r(A<->G){all}   0.285420    0.000342    0.249300    0.321306    0.285103   1055.63   1062.70    1.000
r(A<->T){all}   0.074786    0.000151    0.052861    0.100623    0.074104    873.86    910.56    1.000
r(C<->G){all}   0.036105    0.000031    0.025242    0.046710    0.035938   1081.87   1113.50    1.000
r(C<->T){all}   0.439101    0.000457    0.398411    0.481300    0.439469    880.89    909.47    1.000
r(G<->T){all}   0.070969    0.000084    0.053797    0.089608    0.070723   1111.97   1133.10    1.002
pi(A){all}      0.235698    0.000055    0.221536    0.250448    0.235660    676.27    921.50    1.000
pi(C){all}      0.283781    0.000061    0.268898    0.298724    0.283725   1032.40   1096.39    1.000
pi(G){all}      0.295730    0.000063    0.280527    0.311422    0.295661   1071.16   1111.11    1.000
pi(T){all}      0.184791    0.000041    0.172086    0.196821    0.184738    891.83   1027.14    1.000
alpha{1,2}      0.123388    0.000053    0.109698    0.137965    0.123154   1291.76   1396.38    1.000
alpha{3}        5.252987    1.154853    3.229533    7.345893    5.140676   1158.58   1172.33    1.000
pinvar{all}     0.375986    0.000472    0.334710    0.419216    0.376050   1344.00   1395.07    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	-9281.48237
Model 2: PositiveSelection	-9281.482466
Model 0: one-ratio	-9355.132281
Model 3: discrete	-9266.787676
Model 7: beta	-9268.495154
Model 8: beta&w>1	-9264.543014


Model 0 vs 1	147.29982200000086

Model 2 vs 1	1.919999995152466E-4

Model 8 vs 7	7.904279999998835

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_Sudx-PA)

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

    21 T      0.716         1.154
   187 A      0.944         1.448
   324 P      0.981*        1.494

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_Sudx-PA)

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

    21 T      0.794         1.326 +- 0.409
   185 P      0.645         1.155 +- 0.514
   187 A      0.912         1.446 +- 0.299
   233 G      0.691         1.207 +- 0.495
   322 G      0.657         1.168 +- 0.509
   323 P      0.650         1.161 +- 0.512
   324 P      0.956*        1.487 +- 0.244