--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sun Nov 05 06:00:17 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/vp35/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp35/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/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -5647.39 -5682.83
2 -5647.58 -5685.17
--------------------------------------
TOTAL -5647.48 -5684.57
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp35/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/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 4.390524 0.106451 3.815348 5.067019 4.380022 758.61 817.83 1.000
r(A<->C){all} 0.096736 0.000227 0.067460 0.126552 0.096330 803.28 885.90 1.001
r(A<->G){all} 0.379942 0.000894 0.323439 0.436753 0.378891 711.15 727.13 1.001
r(A<->T){all} 0.065118 0.000159 0.039865 0.088824 0.064854 984.45 987.69 1.001
r(C<->G){all} 0.016982 0.000100 0.000832 0.036035 0.015748 770.05 906.22 1.001
r(C<->T){all} 0.385830 0.000898 0.326438 0.442239 0.385809 676.48 747.90 1.001
r(G<->T){all} 0.055392 0.000194 0.028628 0.082754 0.054977 799.81 802.77 1.001
pi(A){all} 0.329823 0.000111 0.309499 0.350440 0.329755 855.79 946.28 1.000
pi(C){all} 0.231115 0.000087 0.212948 0.249007 0.231157 770.61 897.13 1.001
pi(G){all} 0.200227 0.000077 0.183488 0.217448 0.200105 991.86 1010.61 1.000
pi(T){all} 0.238835 0.000091 0.220368 0.257414 0.238710 1119.16 1130.32 1.000
alpha{1,2} 0.200565 0.000255 0.171117 0.232789 0.199559 1010.29 1175.20 1.000
alpha{3} 4.284052 0.959495 2.629606 6.271498 4.174216 1180.99 1267.07 1.000
pinvar{all} 0.017900 0.000179 0.000001 0.043691 0.015084 986.04 1186.90 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 -5099.552346
Model 2: PositiveSelection -5099.552346
Model 0: one-ratio -5228.980528
Model 3: discrete -5055.113527
Model 7: beta -5055.916397
Model 8: beta&w>1 -5055.916487
Model 0 vs 1 258.8563639999993
Model 2 vs 1 0.0
Model 8 vs 7 1.8000000090978574E-4
