--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Tue Nov 22 01:18:42 WET 2016
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=CLUSTALW2
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/ADOPS/3/AcCoAS-PD/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/3/AcCoAS-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/AcCoAS-PD/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/3/AcCoAS-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -6712.25 -6734.41
2 -6712.58 -6729.16
--------------------------------------
TOTAL -6712.40 -6733.72
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/3/AcCoAS-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/AcCoAS-PD/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/3/AcCoAS-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.122917 0.004374 0.999246 1.253751 1.120666 1243.60 1326.39 1.000
r(A<->C){all} 0.098547 0.000178 0.073212 0.124985 0.098247 1160.25 1224.78 1.000
r(A<->G){all} 0.247285 0.000499 0.202732 0.290572 0.246776 792.37 832.68 1.001
r(A<->T){all} 0.097003 0.000311 0.063238 0.130673 0.096400 734.49 968.75 1.000
r(C<->G){all} 0.055660 0.000061 0.041805 0.071895 0.055304 1118.21 1129.79 1.001
r(C<->T){all} 0.434944 0.000637 0.383508 0.481242 0.435020 838.18 857.98 1.000
r(G<->T){all} 0.066561 0.000120 0.045318 0.087364 0.065886 1102.74 1132.16 1.002
pi(A){all} 0.210187 0.000077 0.193068 0.227262 0.209975 1033.01 1079.86 1.000
pi(C){all} 0.292864 0.000090 0.274577 0.311411 0.292768 1206.95 1274.11 1.000
pi(G){all} 0.289915 0.000093 0.271278 0.308780 0.289675 1122.85 1236.92 1.000
pi(T){all} 0.207034 0.000066 0.192026 0.223178 0.206837 1116.00 1224.99 1.000
alpha{1,2} 0.103149 0.000051 0.089704 0.116940 0.102932 1078.21 1181.94 1.000
alpha{3} 5.094502 1.187664 3.024922 7.181953 4.979400 1501.00 1501.00 1.000
pinvar{all} 0.409786 0.000654 0.361929 0.461384 0.410158 1306.07 1350.63 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 -6181.540846
Model 2: PositiveSelection -6181.540848
Model 0: one-ratio -6199.828236
Model 3: discrete -6177.589209
Model 7: beta -6181.121194
Model 8: beta&w>1 -6177.575576
Model 0 vs 1 36.57478000000083
Model 2 vs 1 3.99999953515362E-6
Model 8 vs 7 7.091236000000208
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: D_melanogaster_AcCoAS-PD)
Pr(w>1) post mean +- SE for w
422 Y 0.501 1.211 +- 0.814
