--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Feb 13 13:01:50 WET 2016
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=/usr/bin/
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb
tcoffee.bin=t_coffee
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_1/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_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/ADOPS/DATA/Zika/B4_A/Zika-NS5_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -9221.12 -9313.56
2 -9222.38 -9318.18
--------------------------------------
TOTAL -9221.56 -9317.50
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_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/ADOPS/DATA/Zika/B4_A/Zika-NS5_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} 1.086105 0.003582 0.970288 1.200607 1.084150 243.81 452.44 1.000
r(A<->C){all} 0.023797 0.000021 0.015474 0.032980 0.023493 686.89 725.34 1.000
r(A<->G){all} 0.185831 0.000328 0.152072 0.219957 0.185444 336.50 343.67 1.002
r(A<->T){all} 0.025585 0.000027 0.015881 0.035774 0.025256 561.72 602.54 1.000
r(C<->G){all} 0.006772 0.000006 0.002605 0.011406 0.006540 839.77 843.92 1.001
r(C<->T){all} 0.737604 0.000456 0.697050 0.777824 0.737535 290.23 321.07 1.001
r(G<->T){all} 0.020410 0.000020 0.012347 0.029152 0.020211 646.78 671.52 1.000
pi(A){all} 0.281247 0.000065 0.266327 0.297671 0.281022 642.89 783.45 1.003
pi(C){all} 0.229648 0.000047 0.215688 0.242565 0.229772 726.08 880.50 1.000
pi(G){all} 0.293509 0.000064 0.278802 0.309439 0.293509 755.10 780.12 1.001
pi(T){all} 0.195595 0.000044 0.183774 0.209850 0.195312 835.94 933.52 1.000
alpha{1,2} 0.124226 0.000080 0.107248 0.142570 0.123852 772.87 946.53 1.000
alpha{3} 4.775503 1.087070 2.830874 6.864657 4.632361 1181.58 1203.17 1.000
pinvar{all} 0.275870 0.000839 0.220134 0.331123 0.276253 976.78 997.42 1.001
------------------------------------------------------------------------------------------------------
* 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 -8681.39429
Model 2: PositiveSelection -8670.732763
Model 0: one-ratio -8741.56394
Model 3: discrete -8664.850351
Model 7: beta -8681.346316
Model 8: beta&w>1 -8664.695611
Model 0 vs 1 120.33929999999964
Model 2 vs 1 21.32305400000041
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: gb:KY272987|Organism:Zika virus|Strain Name:SI-BKK01|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5)
Pr(w>1) post mean +- SE for w
517 R 1.000** 13.998
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:KY272987|Organism:Zika virus|Strain Name:SI-BKK01|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5)
Pr(w>1) post mean +- SE for w
73 Y 0.502 1.182 +- 0.460
200 Y 0.651 1.351 +- 0.352
277 N 0.516 1.266 +- 0.284
284 S 0.642 1.344 +- 0.309
286 H 0.597 1.313 +- 0.324
292 F 0.512 1.194 +- 0.456
517 R 0.974* 1.540 +- 0.415
564 Q 0.508 1.189 +- 0.461
814 T 0.603 1.320 +- 0.302
Model 8 vs 7 33.30141000000003
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: gb:KY272987|Organism:Zika virus|Strain Name:SI-BKK01|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5)
Pr(w>1) post mean +- SE for w
517 R 1.000** 13.585
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:KY272987|Organism:Zika virus|Strain Name:SI-BKK01|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5)
Pr(w>1) post mean +- SE for w
73 Y 0.613 1.080 +- 0.563
138 P 0.566 1.023 +- 0.578
200 Y 0.856 1.371 +- 0.352
277 N 0.732 1.254 +- 0.432
284 S 0.877 1.397 +- 0.313
286 H 0.796 1.311 +- 0.408
292 F 0.628 1.098 +- 0.557
517 R 0.999** 1.507 +- 0.090
564 Q 0.620 1.089 +- 0.561
702 H 0.581 1.042 +- 0.573
814 T 0.839 1.360 +- 0.352
