--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Nov 21 21:05:04 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-PF/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/3/ACC-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/ACC-PF/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-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -26623.95 -26642.92
2 -26623.15 -26639.50
--------------------------------------
TOTAL -26623.47 -26642.26
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/3/ACC-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/ACC-PF/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-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.573215 0.001768 1.490235 1.654664 1.572249 1120.50 1292.65 1.000
r(A<->C){all} 0.082297 0.000035 0.070574 0.093553 0.082202 1046.24 1098.95 1.002
r(A<->G){all} 0.313229 0.000136 0.292007 0.336669 0.312727 720.83 754.45 1.002
r(A<->T){all} 0.113235 0.000078 0.096282 0.130320 0.112834 942.61 976.91 1.000
r(C<->G){all} 0.042193 0.000011 0.035855 0.048217 0.042125 890.70 966.51 1.000
r(C<->T){all} 0.386156 0.000147 0.362119 0.409767 0.386048 597.41 653.76 1.000
r(G<->T){all} 0.062890 0.000025 0.053295 0.072673 0.062734 952.47 1049.70 1.000
pi(A){all} 0.211257 0.000021 0.202273 0.220059 0.211330 699.29 755.83 1.000
pi(C){all} 0.290236 0.000025 0.280494 0.299757 0.290204 767.64 859.72 1.000
pi(G){all} 0.284784 0.000025 0.274627 0.294515 0.284894 713.26 766.30 1.000
pi(T){all} 0.213723 0.000019 0.205224 0.222305 0.213588 787.01 864.52 1.000
alpha{1,2} 0.091164 0.000010 0.085219 0.097377 0.091094 1079.61 1188.41 1.000
alpha{3} 7.769589 1.454497 5.461478 10.076630 7.663893 1268.47 1323.75 1.000
pinvar{all} 0.292227 0.000192 0.265819 0.320015 0.292154 1232.12 1366.56 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-PF)
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
