--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 03 21:02:43 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/revmuscle/S24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S24/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/revmuscle/S24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -7299.74 -7324.22
2 -7299.62 -7320.89
--------------------------------------
TOTAL -7299.68 -7323.56
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/revmuscle/S24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S24/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/revmuscle/S24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.526172 0.003975 1.401025 1.646728 1.525765 1490.11 1495.55 1.000
r(A<->C){all} 0.119419 0.000141 0.097322 0.143094 0.118867 607.85 769.50 1.000
r(A<->G){all} 0.298933 0.000331 0.263852 0.334001 0.298466 858.48 869.35 1.000
r(A<->T){all} 0.074262 0.000057 0.060008 0.089341 0.073752 1055.82 1203.40 1.001
r(C<->G){all} 0.154746 0.000244 0.125397 0.185798 0.154099 829.69 890.90 1.000
r(C<->T){all} 0.267171 0.000302 0.233586 0.301605 0.266739 630.14 690.37 1.000
r(G<->T){all} 0.085468 0.000085 0.067959 0.103200 0.084985 842.46 960.21 1.000
pi(A){all} 0.293028 0.000116 0.272573 0.314161 0.293069 1065.70 1135.79 1.000
pi(C){all} 0.174873 0.000076 0.157566 0.191642 0.174665 1175.14 1176.77 1.000
pi(G){all} 0.196732 0.000086 0.179797 0.216285 0.196555 968.97 1078.30 1.000
pi(T){all} 0.335367 0.000132 0.311555 0.356059 0.335312 1036.07 1162.47 1.000
alpha{1,2} 0.763396 0.014241 0.566847 1.016668 0.747600 1099.68 1291.73 1.000
alpha{3} 2.360759 0.398417 1.274220 3.588140 2.256517 1233.25 1289.72 1.000
pinvar{all} 0.048625 0.001381 0.000029 0.118790 0.040283 1053.27 1192.57 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 -3367.119516
Model 2: PositiveSelection -3344.39726
Model 0: one-ratio -3441.109162
Model 3: discrete -3344.185046
Model 7: beta -3369.288535
Model 8: beta&w>1 -3343.969934
Model 0 vs 1 147.979292
Model 2 vs 1 45.44451200000003
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
2 E 0.983* 4.288
50 I 0.999** 4.344
52 T 0.999** 4.344
69 Q 0.530 2.773
84 Y 0.544 2.820
113 E 0.970* 4.246
115 C 0.966* 4.232
131 T 1.000** 4.345
133 E 0.897 4.001
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
2 E 0.980* 4.516 +- 0.959
50 I 0.999** 4.584 +- 0.829
52 T 0.999** 4.584 +- 0.828
113 E 0.950 4.378 +- 1.101
115 C 0.955* 4.416 +- 1.088
131 T 1.000** 4.586 +- 0.825
133 E 0.855 4.013 +- 1.437
Model 8 vs 7 50.63720199999989
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
2 E 0.988* 3.744
42 R 0.641 2.751
50 I 1.000** 3.778
52 T 1.000** 3.778
69 Q 0.662 2.806
84 Y 0.728 3.003
113 E 0.984* 3.733
115 C 0.979* 3.719
131 T 1.000** 3.778
133 E 0.941 3.610
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
2 E 0.986* 3.942 +- 0.866
42 R 0.550 2.458 +- 1.513
50 I 0.999** 3.981 +- 0.796
52 T 1.000** 3.981 +- 0.795
69 Q 0.603 2.671 +- 1.572
84 Y 0.637 2.736 +- 1.497
113 E 0.975* 3.896 +- 0.910
115 C 0.974* 3.898 +- 0.923
131 T 1.000** 3.982 +- 0.795
133 E 0.917 3.700 +- 1.126
