--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat May 05 18:19:45 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_N1/NS1_3/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_N1/NS1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N1/NS1_3/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_N1/NS1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -8659.23 -8701.67
2 -8655.30 -8708.49
--------------------------------------
TOTAL -8655.98 -8707.79
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_N1/NS1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N1/NS1_3/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_N1/NS1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 7.217333 0.196450 6.341859 8.071543 7.200145 618.81 622.71 1.000
r(A<->C){all} 0.034323 0.000029 0.024379 0.045093 0.034057 890.21 948.28 1.000
r(A<->G){all} 0.208871 0.000253 0.177440 0.238838 0.208254 566.79 577.37 1.000
r(A<->T){all} 0.050874 0.000044 0.038052 0.064030 0.050715 943.50 965.61 1.000
r(C<->G){all} 0.029970 0.000043 0.017690 0.042647 0.029464 802.83 877.05 1.000
r(C<->T){all} 0.652539 0.000388 0.612843 0.689476 0.652902 599.27 652.44 1.000
r(G<->T){all} 0.023423 0.000050 0.009930 0.037240 0.023040 829.69 829.96 1.000
pi(A){all} 0.345922 0.000108 0.325470 0.366320 0.345531 798.16 841.71 1.001
pi(C){all} 0.228843 0.000075 0.212410 0.246066 0.228635 879.90 902.70 1.000
pi(G){all} 0.227934 0.000086 0.209420 0.245739 0.227872 787.64 839.53 1.000
pi(T){all} 0.197301 0.000062 0.181947 0.212601 0.197288 823.47 840.55 1.001
alpha{1,2} 0.201507 0.000179 0.175757 0.226154 0.200465 1072.30 1236.19 1.001
alpha{3} 6.006094 1.250435 3.997584 8.220455 5.909205 1291.27 1392.20 1.000
pinvar{all} 0.121053 0.000483 0.078434 0.162645 0.120570 1326.87 1342.95 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 -7919.185132
Model 2: PositiveSelection -7919.185132
Model 0: one-ratio -8024.578286
Model 3: discrete -7839.173789
Model 7: beta -7847.991435
Model 8: beta&w>1 -7844.357375
Model 0 vs 1 210.78630800000064
Model 2 vs 1 0.0
Model 8 vs 7 7.268120000000636
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:JN851128|Organism:Dengue_virus_2|Strain_Name:SGEHI(D2)0232Y06|Protein_Name:Nonstructural_protein_NS1|Gene_Symbol:NS1)
Pr(w>1) post mean +- SE for w
97 Q 0.738 1.296 +- 0.395
126 L 0.601 1.159 +- 0.442
