--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat May 26 02:47:28 WEST 2018
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
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/ADOPS1/DNG_A1/NS1_2/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_A1/NS1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS1_2/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/ADOPS1/DNG_A1/NS1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -9265.11 -9307.68
2 -9266.12 -9305.59
--------------------------------------
TOTAL -9265.49 -9307.11
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_A1/NS1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS1_2/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/ADOPS1/DNG_A1/NS1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 7.970151 0.237967 7.019284 8.910147 7.950069 836.22 919.31 1.000
r(A<->C){all} 0.028854 0.000023 0.019698 0.038464 0.028727 860.12 961.97 1.000
r(A<->G){all} 0.245284 0.000300 0.212765 0.279057 0.244863 521.38 523.02 1.004
r(A<->T){all} 0.053745 0.000043 0.041244 0.066283 0.053517 687.98 730.23 1.001
r(C<->G){all} 0.024734 0.000035 0.013521 0.036114 0.024344 796.90 827.17 1.000
r(C<->T){all} 0.624602 0.000421 0.583005 0.662000 0.624501 479.35 491.79 1.005
r(G<->T){all} 0.022782 0.000041 0.010718 0.035672 0.022400 670.79 748.34 1.000
pi(A){all} 0.353789 0.000110 0.332998 0.373788 0.353559 780.98 812.23 1.003
pi(C){all} 0.231192 0.000077 0.213862 0.248331 0.231200 561.47 735.84 1.001
pi(G){all} 0.219098 0.000078 0.202218 0.236702 0.219123 486.90 509.10 1.000
pi(T){all} 0.195920 0.000063 0.181301 0.211649 0.195798 624.57 661.46 1.003
alpha{1,2} 0.194928 0.000149 0.172175 0.219697 0.193979 1257.51 1295.19 1.000
alpha{3} 4.445273 0.607220 3.090996 5.975314 4.362642 1432.62 1438.00 1.002
pinvar{all} 0.132247 0.000503 0.089100 0.175918 0.132460 1160.43 1251.31 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 -8913.519685
Model 2: PositiveSelection -8913.519685
Model 0: one-ratio -9056.978282
Model 3: discrete -8808.369922
Model 7: beta -8818.46621
Model 8: beta&w>1 -8807.758727
Model 0 vs 1 286.9171940000015
Model 2 vs 1 0.0
Model 8 vs 7 21.414966000000277
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: gb:KY586424|Organism:Dengue_virus|Strain_Name:Ser1_Thailand_BangkokSeq_99|Protein_Name:nonstructural_protein_1|Gene_Symbol:NS1)
Pr(w>1) post mean +- SE for w
98 G 0.790 1.328 +- 0.346
128 V 0.775 1.316 +- 0.351
131 S 0.541 1.098 +- 0.452
178 V 0.834 1.364 +- 0.320
224 I 0.510 1.066 +- 0.459
