--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Nov 21 16:35:44 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/3/ACC-PC/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/3/ACC-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/ACC-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/3/ACC-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -26623.68 -26641.93
2 -26623.79 -26642.60
--------------------------------------
TOTAL -26623.73 -26642.32
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/3/ACC-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/ACC-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/3/ACC-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} 1.573264 0.001804 1.495471 1.659774 1.572764 1354.62 1356.66 1.000
r(A<->C){all} 0.082248 0.000034 0.070621 0.093093 0.082331 879.11 1009.85 1.000
r(A<->G){all} 0.313411 0.000132 0.290646 0.335403 0.313446 767.11 920.42 1.000
r(A<->T){all} 0.113105 0.000075 0.096776 0.130174 0.113066 642.98 772.00 1.000
r(C<->G){all} 0.042181 0.000011 0.035286 0.048481 0.042094 959.19 1042.12 1.000
r(C<->T){all} 0.385873 0.000146 0.362370 0.410283 0.385761 678.31 699.49 1.000
r(G<->T){all} 0.063181 0.000024 0.053665 0.072696 0.063027 972.68 1011.42 1.000
pi(A){all} 0.211309 0.000022 0.202558 0.220713 0.211353 873.30 942.37 1.000
pi(C){all} 0.290136 0.000022 0.280997 0.299088 0.290063 1043.83 1177.90 1.000
pi(G){all} 0.284877 0.000024 0.275321 0.294607 0.284679 870.20 904.41 1.001
pi(T){all} 0.213678 0.000019 0.205192 0.222091 0.213596 531.25 806.71 1.002
alpha{1,2} 0.091149 0.000010 0.085312 0.097479 0.091061 1385.04 1443.02 1.000
alpha{3} 7.809226 1.477869 5.665973 10.377980 7.690800 1313.49 1397.25 1.000
pinvar{all} 0.292115 0.000180 0.265606 0.318286 0.292330 1086.92 1188.77 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 -24565.669304
Model 2: PositiveSelection -24565.669356
Model 0: one-ratio -24706.841833
Model 3: discrete -24514.70771
Model 7: beta -24531.162641
Model 8: beta&w>1 -24523.020789
Model 0 vs 1 282.34505799999897
Model 2 vs 1 1.0399999882793054E-4
Model 8 vs 7 16.283704000001308
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_ACC-PC)
Pr(w>1) post mean +- SE for w
280 N 0.655 1.196 +- 0.433
752 S 0.734 1.265 +- 0.410
757 Y 0.563 1.079 +- 0.499
815 L 0.692 1.220 +- 0.437
2136 A 0.515 1.026 +- 0.510
