--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Nov 21 14:03:34 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-PB/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/3/ACC-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/ACC-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/3/ACC-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -26622.08 -26643.25
2 -26623.77 -26641.26
--------------------------------------
TOTAL -26622.61 -26642.68
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/3/ACC-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/ACC-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/3/ACC-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} 1.572864 0.001844 1.487657 1.654629 1.571973 1320.81 1410.90 1.000
r(A<->C){all} 0.082497 0.000034 0.070955 0.093833 0.082220 910.52 1002.91 1.000
r(A<->G){all} 0.314054 0.000131 0.293011 0.336018 0.313619 866.74 894.03 1.000
r(A<->T){all} 0.113188 0.000077 0.094955 0.129599 0.113062 983.01 1050.30 1.000
r(C<->G){all} 0.042194 0.000011 0.035776 0.048369 0.042126 1113.83 1118.42 1.000
r(C<->T){all} 0.385143 0.000142 0.360243 0.406597 0.385129 801.07 873.93 1.000
r(G<->T){all} 0.062924 0.000025 0.053481 0.072691 0.062688 1064.02 1098.75 1.001
pi(A){all} 0.210983 0.000020 0.201901 0.219119 0.211025 927.85 939.39 1.000
pi(C){all} 0.290154 0.000023 0.280085 0.299172 0.290047 918.93 1002.66 1.000
pi(G){all} 0.284796 0.000024 0.275630 0.294350 0.284856 882.53 912.29 1.000
pi(T){all} 0.214067 0.000019 0.204823 0.221968 0.214157 737.54 779.36 1.000
alpha{1,2} 0.091150 0.000009 0.085180 0.097121 0.091079 1231.52 1253.72 1.000
alpha{3} 7.805217 1.491383 5.679169 10.356290 7.679660 1336.24 1418.62 1.000
pinvar{all} 0.292626 0.000197 0.266299 0.321154 0.292798 1303.99 1368.61 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 -24565.66932
Model 0: one-ratio -24706.841833
Model 3: discrete -24513.827021
Model 7: beta -24531.162579
Model 8: beta&w>1 -24523.020721
Model 0 vs 1 282.34505799999897
Model 2 vs 1 3.2000003557186574E-5
Model 8 vs 7 16.283715999998094
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-PB)
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
