--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Nov 21 18:38:33 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/295/Lnk-PB/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/295/Lnk-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/295/Lnk-PB/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/295/Lnk-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -8839.22         -8860.25
2      -8840.70         -8859.68
--------------------------------------
TOTAL    -8839.71         -8860.00
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/295/Lnk-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/295/Lnk-PB/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/295/Lnk-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.287773    0.004878    1.150280    1.424896    1.287110   1459.31   1480.15    1.000
r(A<->C){all}   0.106563    0.000120    0.084778    0.127458    0.106175   1015.72   1116.37    1.000
r(A<->G){all}   0.215904    0.000283    0.180668    0.247118    0.216001    874.12    900.12    1.000
r(A<->T){all}   0.125174    0.000224    0.095898    0.154783    0.124685   1106.27   1144.86    1.000
r(C<->G){all}   0.075111    0.000066    0.059770    0.091412    0.074788    943.13   1069.18    1.000
r(C<->T){all}   0.404663    0.000491    0.359532    0.445888    0.404566    744.52    772.36    1.000
r(G<->T){all}   0.072585    0.000103    0.053422    0.092756    0.072192    924.07   1039.04    1.000
pi(A){all}      0.233590    0.000068    0.218395    0.250840    0.233624   1092.26   1097.14    1.000
pi(C){all}      0.293118    0.000079    0.275755    0.310442    0.293029    920.87    987.37    1.000
pi(G){all}      0.296369    0.000084    0.279361    0.315628    0.296290   1070.01   1080.12    1.000
pi(T){all}      0.176922    0.000054    0.163066    0.191290    0.176753    812.38    895.29    1.000
alpha{1,2}      0.165352    0.000136    0.143367    0.187788    0.164705   1289.99   1330.27    1.000
alpha{3}        4.578154    0.942142    2.836384    6.571339    4.448044   1480.95   1490.98    1.000
pinvar{all}     0.367865    0.000631    0.318930    0.418231    0.367992   1258.34   1341.16    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	-7916.756018
Model 2: PositiveSelection	-7916.756039
Model 0: one-ratio	-7992.480109
Model 3: discrete	-7907.483779
Model 7: beta	-7913.023214
Model 8: beta&w>1	-7908.266947


Model 0 vs 1	151.4481820000001

Model 2 vs 1	4.199999966658652E-5

Model 8 vs 7	9.512533999999505

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_Lnk-PB)

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

    36 A      0.731         1.131
   323 S      0.940         1.372
   531 S      0.608         0.986
   543 N      0.932         1.362
   571 S      0.563         0.934
   576 T      0.700         1.094
   681 G      0.991**       1.429

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_Lnk-PB)

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

    36 A      0.804         1.325 +- 0.377
   323 S      0.918         1.436 +- 0.245
   531 S      0.770         1.282 +- 0.423
   543 N      0.917         1.434 +- 0.249
   571 S      0.741         1.252 +- 0.444
   576 T      0.790         1.310 +- 0.390
   681 G      0.972*        1.483 +- 0.150