--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Oct 27 00:20:25 WEST 2017
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/Ebola_B1_2/NP/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1_2/NP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1_2/NP/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/Ebola_B1_2/NP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -13775.91 -13850.02
2 -13780.56 -13865.14
--------------------------------------
TOTAL -13776.60 -13864.44
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1_2/NP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1_2/NP/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/Ebola_B1_2/NP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 4.981023 0.076030 4.450105 5.522384 4.970749 169.52 246.77 1.001
r(A<->C){all} 0.122897 0.000104 0.104722 0.144401 0.122747 530.45 606.89 1.002
r(A<->G){all} 0.326298 0.000331 0.291011 0.361456 0.326337 340.16 434.23 1.000
r(A<->T){all} 0.039391 0.000053 0.025138 0.053613 0.038967 637.68 673.82 1.000
r(C<->G){all} 0.023533 0.000045 0.010569 0.036456 0.023273 605.90 670.95 1.000
r(C<->T){all} 0.435949 0.000388 0.397447 0.472454 0.436228 423.28 452.72 1.000
r(G<->T){all} 0.051933 0.000067 0.037093 0.068698 0.051838 418.05 518.72 1.001
pi(A){all} 0.314452 0.000050 0.300631 0.327881 0.314421 774.02 789.37 1.002
pi(C){all} 0.237216 0.000038 0.225395 0.248985 0.237149 374.67 573.57 1.000
pi(G){all} 0.219354 0.000037 0.207012 0.230946 0.219283 534.97 643.21 1.000
pi(T){all} 0.228978 0.000039 0.216892 0.240491 0.228774 825.70 888.11 1.004
alpha{1,2} 0.204389 0.000125 0.183448 0.226197 0.204100 502.07 570.98 1.001
alpha{3} 4.224573 0.690204 2.733981 5.836078 4.110626 889.58 1032.39 1.000
pinvar{all} 0.034537 0.000184 0.007214 0.060049 0.034642 908.91 969.15 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 -12761.551714
Model 2: PositiveSelection -12761.551679
Model 0: one-ratio -13241.1815
Model 3: discrete -12686.233508
Model 7: beta -12694.623125
Model 8: beta&w>1 -12688.712295
Model 0 vs 1 959.2595720000027
Model 2 vs 1 6.999999823165126E-5
Model 8 vs 7 11.82166000000143
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:KU143801:56-3026|Organism:Zaire ebolavirus|Strain Name:Ebola virus H.sapiens-wt/SLE/2014/Makona-S33|Protein Name:nucleprotein|Gene Symbol:NP)
Pr(w>1) post mean +- SE for w
536 H 0.829 3.274
540 P 0.503 2.199
541 L 0.840 3.313
542 T 0.999** 3.824
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:KU143801:56-3026|Organism:Zaire ebolavirus|Strain Name:Ebola virus H.sapiens-wt/SLE/2014/Makona-S33|Protein Name:nucleprotein|Gene Symbol:NP)
Pr(w>1) post mean +- SE for w
111 C 0.728 1.284 +- 0.371
504 G 0.532 1.111 +- 0.437
516 T 0.722 1.291 +- 0.351
536 H 0.892 1.423 +- 0.230
537 A 0.664 1.222 +- 0.409
540 P 0.745 1.291 +- 0.375
541 L 0.906 1.435 +- 0.208
542 T 0.981* 1.488 +- 0.090
549 G 0.544 1.125 +- 0.433
550 S 0.541 1.128 +- 0.425
574 S 0.543 1.126 +- 0.430
619 Q 0.593 1.178 +- 0.407
