--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Sep 29 05:24:47 WEST 2017
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/ADOPS1/ASP1/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/ASP1/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/ASP1/ClustalW2/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/ASP1/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -11375.06 -11433.98
2 -11374.67 -11436.60
--------------------------------------
TOTAL -11374.84 -11435.98
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/ASP1/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/ASP1/ClustalW2/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/ASP1/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 15.989573 0.778511 14.342760 17.763120 15.982220 644.77 710.78 1.000
r(A<->C){all} 0.065064 0.000079 0.047897 0.081700 0.064687 247.02 347.70 1.000
r(A<->G){all} 0.288662 0.000528 0.247687 0.339218 0.287788 122.14 148.37 1.000
r(A<->T){all} 0.079213 0.000072 0.062098 0.095351 0.078794 198.38 345.14 1.000
r(C<->G){all} 0.069071 0.000103 0.050607 0.089123 0.068486 338.57 423.25 1.001
r(C<->T){all} 0.320775 0.000556 0.272428 0.365624 0.320839 104.38 130.91 1.000
r(G<->T){all} 0.177214 0.000212 0.149051 0.205834 0.176951 353.13 365.46 1.000
pi(A){all} 0.217401 0.000162 0.191721 0.241587 0.217229 248.91 261.42 1.000
pi(C){all} 0.264986 0.000123 0.243987 0.287186 0.265164 210.22 278.47 1.000
pi(G){all} 0.158398 0.000125 0.136733 0.179248 0.158176 124.32 168.58 1.000
pi(T){all} 0.359215 0.000180 0.333236 0.385040 0.358817 195.03 212.64 1.000
alpha{1,2} 0.544395 0.001351 0.474182 0.617942 0.544140 881.23 1035.37 1.000
alpha{3} 0.669775 0.002347 0.569779 0.761964 0.668596 688.51 858.56 1.001
pinvar{all} 0.338157 0.000551 0.290867 0.381309 0.338230 802.41 965.66 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 -6337.020012
Model 2: PositiveSelection -6228.794468
Model 0: one-ratio -6683.0048
Model 3: discrete -6226.583334
Model 7: beta -6333.602326
Model 8: beta&w>1 -6221.989614
Model 0 vs 1 691.9695759999995
Model 2 vs 1 216.4510879999998
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 01_AE.AF.07.569M.GQ477441)
Pr(w>1) post mean +- SE for w
9 I 1.000** 4.356
103 S 0.999** 4.353
107 P 1.000** 4.356
119 T 1.000** 4.356
120 Q 0.998** 4.349
123 I 1.000** 4.356
125 L 0.999** 4.354
135 A 1.000** 4.356
151 S 0.827 3.777
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: 01_AE.AF.07.569M.GQ477441)
Pr(w>1) post mean +- SE for w
9 I 1.000** 4.499 +- 0.233
103 S 0.999** 4.494 +- 0.268
107 P 1.000** 4.499 +- 0.233
119 T 1.000** 4.499 +- 0.233
120 Q 0.998** 4.491 +- 0.291
123 I 1.000** 4.499 +- 0.233
125 L 0.999** 4.497 +- 0.251
135 A 0.999** 4.497 +- 0.246
151 S 0.757 3.625 +- 1.497
Model 8 vs 7 223.2254240000002
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 01_AE.AF.07.569M.GQ477441)
Pr(w>1) post mean +- SE for w
9 I 1.000** 3.920
103 S 1.000** 3.919
107 P 1.000** 3.920
119 T 1.000** 3.920
120 Q 0.999** 3.917
123 I 1.000** 3.920
125 L 1.000** 3.918
135 A 1.000** 3.919
141 I 0.548 2.550
151 S 0.950* 3.769
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: 01_AE.AF.07.569M.GQ477441)
Pr(w>1) post mean +- SE for w
9 I 1.000** 4.097 +- 0.494
103 S 0.999** 4.092 +- 0.508
107 P 1.000** 4.097 +- 0.494
119 T 1.000** 4.097 +- 0.494
120 Q 0.998** 4.089 +- 0.518
123 I 1.000** 4.097 +- 0.494
125 L 0.999** 4.094 +- 0.502
135 A 0.999** 4.095 +- 0.500
151 S 0.688 2.997 +- 1.446
