--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sun Nov 05 07:36:45 WET 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=
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/Ebolaaminoresults/vp40/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp40/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/Ebolaaminoresults/vp40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -6286.82 -6321.29
2 -6287.20 -6315.91
--------------------------------------
TOTAL -6286.99 -6320.61
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp40/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/Ebolaaminoresults/vp40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 4.047650 0.093518 3.482754 4.652256 4.038287 909.71 1119.77 1.000
r(A<->C){all} 0.123958 0.000245 0.096810 0.157824 0.123320 966.44 1038.56 1.001
r(A<->G){all} 0.385542 0.000805 0.327096 0.437811 0.385541 690.27 777.39 1.000
r(A<->T){all} 0.061770 0.000209 0.034669 0.090605 0.060942 667.14 790.18 1.000
r(C<->G){all} 0.008225 0.000049 0.000001 0.022351 0.006529 728.30 850.79 1.000
r(C<->T){all} 0.355778 0.000784 0.300188 0.408550 0.354920 932.44 934.00 1.001
r(G<->T){all} 0.064727 0.000197 0.037525 0.090991 0.064022 961.59 1007.77 1.000
pi(A){all} 0.270993 0.000077 0.252723 0.287538 0.270824 1131.15 1189.53 1.000
pi(C){all} 0.271410 0.000079 0.254947 0.290143 0.271688 1113.05 1181.10 1.000
pi(G){all} 0.226877 0.000072 0.210325 0.243526 0.226839 1208.63 1269.77 1.000
pi(T){all} 0.230720 0.000069 0.215884 0.247529 0.230548 939.66 946.95 1.000
alpha{1,2} 0.166748 0.000143 0.143714 0.189751 0.165813 938.88 1103.77 1.000
alpha{3} 3.993471 0.811470 2.358286 5.757092 3.880608 1394.17 1447.58 1.000
pinvar{all} 0.035730 0.000455 0.000016 0.073194 0.033683 1460.73 1480.86 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 -4769.53679
Model 2: PositiveSelection -4769.53679
Model 0: one-ratio -4841.668108
Model 3: discrete -4734.507062
Model 7: beta -4737.765685
Model 8: beta&w>1 -4737.766103
Model 0 vs 1 144.26263599999947
Model 2 vs 1 0.0
Model 8 vs 7 8.35999999253545E-4
