--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Nov 23 06:05:41 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/304/mfas-PC/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/304/mfas-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/304/mfas-PC/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/304/mfas-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -9861.33         -9876.59
2      -9860.97         -9879.72
--------------------------------------
TOTAL    -9861.14         -9879.07
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/304/mfas-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/304/mfas-PC/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/304/mfas-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.098946    0.003169    0.989889    1.205202    1.096999   1487.23   1494.12    1.000
r(A<->C){all}   0.133497    0.000146    0.109476    0.156529    0.132795    965.86   1033.01    1.000
r(A<->G){all}   0.243386    0.000354    0.207469    0.279207    0.242965    884.86    952.86    1.006
r(A<->T){all}   0.084496    0.000179    0.058365    0.109183    0.083808    822.74    978.63    1.001
r(C<->G){all}   0.063934    0.000052    0.049875    0.077820    0.063500   1027.52   1113.81    1.000
r(C<->T){all}   0.398670    0.000462    0.357181    0.440914    0.398384    820.58    863.02    1.004
r(G<->T){all}   0.076017    0.000096    0.056755    0.094740    0.075852   1079.98   1216.63    1.001
pi(A){all}      0.209819    0.000058    0.195758    0.225093    0.209737    830.74    992.64    1.000
pi(C){all}      0.332318    0.000071    0.315254    0.348064    0.332290   1079.09   1085.83    1.000
pi(G){all}      0.265357    0.000068    0.249193    0.281257    0.265097    976.60   1028.99    1.000
pi(T){all}      0.192507    0.000046    0.179923    0.206254    0.192412   1178.12   1216.17    1.002
alpha{1,2}      0.155377    0.000117    0.136948    0.179237    0.154987   1220.41   1360.71    1.000
alpha{3}        4.267107    0.847639    2.739064    6.115669    4.151304   1212.18   1356.59    1.000
pinvar{all}     0.382112    0.000619    0.334629    0.432948    0.383454   1187.30   1254.23    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	-9043.140148
Model 2: PositiveSelection	-9043.140304
Model 0: one-ratio	-9136.55821
Model 3: discrete	-9030.689976
Model 7: beta	-9035.925436
Model 8: beta&w>1	-9031.667853


Model 0 vs 1	186.83612399999765

Model 2 vs 1	3.120000001217704E-4

Model 8 vs 7	8.515165999997407

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
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_mfas-PC)

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

    33 A      0.558         1.072 +- 0.500
    83 G      0.568         1.022 +- 0.572
   109 S      0.883         1.402 +- 0.275
   177 S      0.658         1.185 +- 0.450
   181 A      0.678         1.181 +- 0.480
   311 M      0.900         1.415 +- 0.262
   516 H      0.758         1.287 +- 0.386
   537 D      0.771         1.284 +- 0.408
   620 N      0.610         1.125 +- 0.485
   754 N      0.723         1.256 +- 0.405
   760 S      0.789         1.297 +- 0.406