--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri May 25 03:02:23 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_1/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_A1/NS1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS1_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -8578.98 -8625.61
2 -8576.99 -8635.01
--------------------------------------
TOTAL -8577.56 -8634.32
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_A1/NS1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS1_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 7.061918 0.217229 6.119356 7.933400 7.046622 588.49 600.44 1.000
r(A<->C){all} 0.031058 0.000031 0.020392 0.042085 0.030903 704.83 786.88 1.000
r(A<->G){all} 0.227081 0.000289 0.195949 0.260514 0.227040 606.11 660.73 1.000
r(A<->T){all} 0.056509 0.000052 0.043015 0.070569 0.056291 677.10 769.34 1.000
r(C<->G){all} 0.022135 0.000039 0.011028 0.034886 0.021683 709.93 734.92 1.001
r(C<->T){all} 0.635477 0.000411 0.596931 0.674172 0.635463 434.52 575.90 1.000
r(G<->T){all} 0.027740 0.000051 0.014001 0.041716 0.027284 746.40 746.72 1.000
pi(A){all} 0.347892 0.000109 0.327683 0.368054 0.347799 758.57 970.62 1.000
pi(C){all} 0.228362 0.000079 0.209986 0.244634 0.228234 765.18 794.12 1.000
pi(G){all} 0.226861 0.000088 0.209940 0.245728 0.226704 671.77 721.30 1.001
pi(T){all} 0.196886 0.000060 0.180936 0.211466 0.196766 898.71 957.78 1.000
alpha{1,2} 0.208197 0.000178 0.182822 0.233707 0.207404 1266.30 1279.09 1.000
alpha{3} 5.487497 1.109989 3.615456 7.584599 5.368261 1135.16 1318.08 1.000
pinvar{all} 0.139925 0.000532 0.095227 0.185246 0.139287 915.72 1112.14 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 -8230.639844
Model 2: PositiveSelection -8230.639844
Model 0: one-ratio -8359.991238
Model 3: discrete -8150.736716
Model 7: beta -8155.178613
Model 8: beta&w>1 -8151.584891
Model 0 vs 1 258.70278800000233
Model 2 vs 1 0.0
Model 8 vs 7 7.187443999999232
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:FJ410223|Organism:Dengue_virus_2|Strain_Name:DENV-2/VN/BID-V1869/2007|Protein_Name:Nonstructural_protein_NS1|Gene_Symbol:NS1)
Pr(w>1) post mean +- SE for w
94 K 0.679 1.227 +- 0.412
128 S 0.612 1.163 +- 0.438
131 Q 0.753 1.297 +- 0.369
178 F 0.561 1.112 +- 0.455
