--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Dec 05 04:50:20 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/350/Pkcdelta-PD/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/350/Pkcdelta-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/350/Pkcdelta-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/350/Pkcdelta-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -6576.55         -6593.52
2      -6576.33         -6592.04
--------------------------------------
TOTAL    -6576.43         -6593.03
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/350/Pkcdelta-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/350/Pkcdelta-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/350/Pkcdelta-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}         0.849595    0.003104    0.742248    0.957958    0.848366   1501.00   1501.00    1.000
r(A<->C){all}   0.092845    0.000169    0.067428    0.116894    0.092627    926.55    972.43    1.001
r(A<->G){all}   0.253404    0.000560    0.209904    0.301807    0.253111    938.31    964.52    1.000
r(A<->T){all}   0.088228    0.000191    0.062667    0.116073    0.087559   1171.71   1255.36    1.001
r(C<->G){all}   0.070279    0.000107    0.049981    0.090456    0.069668   1110.03   1157.75    1.001
r(C<->T){all}   0.443401    0.000719    0.390469    0.494819    0.443581    851.58    892.80    1.000
r(G<->T){all}   0.051843    0.000096    0.033483    0.071309    0.051249   1139.83   1218.34    1.000
pi(A){all}      0.249619    0.000088    0.230472    0.267183    0.249773    689.22    895.59    1.000
pi(C){all}      0.257112    0.000082    0.240067    0.275247    0.256987   1051.67   1119.47    1.002
pi(G){all}      0.266289    0.000090    0.248112    0.285533    0.266008   1089.92   1092.40    1.000
pi(T){all}      0.226981    0.000073    0.209805    0.243088    0.226804   1045.59   1125.84    1.001
alpha{1,2}      0.144474    0.000154    0.122032    0.169346    0.143691   1277.35   1307.53    1.001
alpha{3}        4.356708    1.059276    2.619300    6.501671    4.242129   1147.51   1309.29    1.000
pinvar{all}     0.497666    0.000636    0.448356    0.545667    0.498477   1308.08   1328.07    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	-5982.71707
Model 2: PositiveSelection	-5982.717136
Model 0: one-ratio	-6011.633126
Model 3: discrete	-5975.812449
Model 7: beta	-5979.246239
Model 8: beta&w>1	-5976.0363


Model 0 vs 1	57.83211200000005

Model 2 vs 1	1.320000010309741E-4

Model 8 vs 7	6.419878000000608

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_Pkcdelta-PD)

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

    96 V      0.935         1.709
    98 I      0.974*        1.771

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_Pkcdelta-PD)

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

    96 V      0.903         1.507 +- 0.461
    98 I      0.940         1.550 +- 0.451