--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Nov 08 17:59:26 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=
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/afazermus/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/afazermus/S24_16SFBBs/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/afazermus/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -7156.56 -7175.36
2 -7156.20 -7173.61
--------------------------------------
TOTAL -7156.36 -7174.83
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/afazermus/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/afazermus/S24_16SFBBs/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/afazermus/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.447229 0.003634 1.335770 1.566210 1.445050 1351.76 1414.83 1.001
r(A<->C){all} 0.120002 0.000147 0.097347 0.144671 0.119452 958.31 1019.37 1.000
r(A<->G){all} 0.301393 0.000377 0.262879 0.338095 0.301383 833.96 869.29 1.000
r(A<->T){all} 0.073112 0.000057 0.058621 0.088271 0.072840 1020.27 1176.74 1.000
r(C<->G){all} 0.155235 0.000242 0.126814 0.187189 0.154745 798.29 911.43 1.000
r(C<->T){all} 0.266778 0.000335 0.231695 0.302710 0.266908 599.68 802.36 1.000
r(G<->T){all} 0.083479 0.000081 0.067219 0.102213 0.083106 1111.91 1177.96 1.001
pi(A){all} 0.294061 0.000116 0.272596 0.315150 0.293560 958.74 1012.23 1.001
pi(C){all} 0.174792 0.000078 0.158384 0.193011 0.174467 984.84 1128.72 1.000
pi(G){all} 0.196583 0.000087 0.178343 0.214911 0.196544 944.00 1109.73 1.003
pi(T){all} 0.334565 0.000127 0.312746 0.356465 0.334628 1035.74 1084.72 1.000
alpha{1,2} 0.789860 0.014972 0.581482 1.035847 0.771309 1223.48 1362.24 1.000
alpha{3} 2.500810 0.495852 1.361102 3.924254 2.362617 1300.59 1331.61 1.000
pinvar{all} 0.050565 0.001313 0.000006 0.119193 0.043952 964.62 1226.54 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 -5182.219563
Model 2: PositiveSelection -5153.400929
Model 0: one-ratio -5293.71354
Model 3: discrete -5153.186482
Model 7: beta -5190.523449
Model 8: beta&w>1 -5153.987351
Model 0 vs 1 222.98795400000017
Model 2 vs 1 57.637267999998585
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S24_SFBB1)
Pr(w>1) post mean +- SE for w
14 N 0.993** 3.468
20 R 0.999** 3.483
24 P 0.973* 3.419
53 L 0.956* 3.375
60 E 0.918 3.281
72 L 0.635 2.578
101 R 0.829 3.059
109 I 0.999** 3.482
111 T 0.999** 3.483
128 Q 0.882 3.191
172 E 0.966* 3.401
174 C 0.853 3.119
190 T 0.998** 3.481
192 E 0.809 3.010
220 K 0.528 2.312
243 T 0.745 2.851
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: S24_SFBB1)
Pr(w>1) post mean +- SE for w
14 N 0.992** 3.589 +- 0.472
20 R 0.999** 3.609 +- 0.416
24 P 0.967* 3.522 +- 0.615
53 L 0.947 3.469 +- 0.708
60 E 0.905 3.362 +- 0.857
72 L 0.577 2.467 +- 1.288
101 R 0.790 3.041 +- 1.108
109 I 0.998** 3.607 +- 0.423
111 T 0.999** 3.609 +- 0.417
128 Q 0.864 3.253 +- 0.970
172 E 0.957* 3.493 +- 0.663
174 C 0.825 3.143 +- 1.051
190 T 0.998** 3.606 +- 0.426
192 E 0.771 2.994 +- 1.140
243 T 0.686 2.752 +- 1.224
Model 8 vs 7 73.07219600000099
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S24_SFBB1)
Pr(w>1) post mean +- SE for w
14 N 0.997** 3.021
20 R 1.000** 3.025
24 P 0.990* 3.005
53 L 0.981* 2.986
58 F 0.667 2.313
60 E 0.959* 2.939
72 L 0.833 2.668
101 R 0.927 2.870
109 I 0.999** 3.025
111 T 1.000** 3.025
128 Q 0.937 2.891
140 Q 0.614 2.183
143 Y 0.596 2.159
157 T 0.690 2.353
172 E 0.988* 3.000
174 C 0.934 2.884
190 T 0.999** 3.024
192 E 0.912 2.836
220 K 0.754 2.496
237 C 0.620 2.214
243 T 0.901 2.815
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: S24_SFBB1)
Pr(w>1) post mean +- SE for w
14 N 0.998** 2.826 +- 0.509
20 R 1.000** 2.831 +- 0.502
24 P 0.990* 2.809 +- 0.533
53 L 0.981* 2.790 +- 0.559
58 F 0.718 2.163 +- 0.870
60 E 0.961* 2.746 +- 0.615
72 L 0.840 2.449 +- 0.801
73 A 0.583 1.883 +- 0.922
85 G 0.505 1.727 +- 0.957
101 R 0.926 2.657 +- 0.684
109 I 0.999** 2.830 +- 0.503
111 T 1.000** 2.831 +- 0.503
128 Q 0.940 2.698 +- 0.667
140 Q 0.669 2.079 +- 0.943
143 Y 0.674 2.073 +- 0.889
157 T 0.727 2.202 +- 0.911
172 E 0.987* 2.802 +- 0.540
174 C 0.936 2.683 +- 0.669
190 T 0.999** 2.830 +- 0.505
192 E 0.913 2.628 +- 0.712
220 K 0.776 2.303 +- 0.859
237 C 0.688 2.091 +- 0.867
243 T 0.896 2.580 +- 0.725
