--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 03 21:35:47 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/S25/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S25/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/S25/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -7218.95 -7236.64
2 -7218.11 -7234.69
--------------------------------------
TOTAL -7218.44 -7236.08
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/revmuscle/S25/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S25/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/S25/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.411342 0.003582 1.296463 1.533146 1.411036 1274.94 1387.97 1.000
r(A<->C){all} 0.117456 0.000142 0.095376 0.141581 0.117231 842.04 916.37 1.002
r(A<->G){all} 0.299580 0.000338 0.266143 0.338348 0.299210 624.49 695.07 1.000
r(A<->T){all} 0.076804 0.000058 0.063491 0.092613 0.076514 969.55 1055.09 1.000
r(C<->G){all} 0.164638 0.000246 0.133911 0.196458 0.164346 865.43 995.16 1.000
r(C<->T){all} 0.255648 0.000290 0.222222 0.287928 0.254916 574.24 659.61 1.000
r(G<->T){all} 0.085873 0.000086 0.067098 0.103020 0.085761 1156.12 1182.96 1.000
pi(A){all} 0.298985 0.000121 0.277162 0.319558 0.298770 1035.82 1045.97 1.000
pi(C){all} 0.172981 0.000074 0.157056 0.190855 0.172902 888.54 982.33 1.000
pi(G){all} 0.190271 0.000083 0.173064 0.208007 0.190062 794.39 884.76 1.000
pi(T){all} 0.337763 0.000131 0.315453 0.360256 0.337689 702.62 877.55 1.000
alpha{1,2} 0.755680 0.011754 0.556234 0.961197 0.743714 1103.79 1143.33 1.000
alpha{3} 1.718519 0.182976 1.014866 2.563881 1.650783 1126.97 1157.92 1.000
pinvar{all} 0.042998 0.001138 0.000003 0.110555 0.035041 1036.51 1078.62 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 -1305.49625
Model 2: PositiveSelection -1292.608656
Model 0: one-ratio -1332.90378
Model 3: discrete -1292.605245
Model 7: beta -1307.095987
Model 8: beta&w>1 -1292.523632
Model 0 vs 1 54.81506000000036
Model 2 vs 1 25.775187999999616
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S25_SFBB1)
Pr(w>1) post mean +- SE for w
7 Q 0.848 3.699
19 Q 0.986* 4.142
22 Y 0.791 3.519
26 A 0.767 3.443
36 T 0.856 3.726
51 E 0.989* 4.150
54 C 1.000** 4.185
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: S25_SFBB1)
Pr(w>1) post mean +- SE for w
7 Q 0.829 3.831 +- 1.653
19 Q 0.984* 4.434 +- 1.267
22 Y 0.714 3.257 +- 1.629
26 A 0.688 3.160 +- 1.635
36 T 0.800 3.628 +- 1.594
51 E 0.977* 4.369 +- 1.249
54 C 1.000** 4.488 +- 1.203
Model 8 vs 7 29.144710000000032
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S25_SFBB1)
Pr(w>1) post mean +- SE for w
7 Q 0.888 3.487
19 Q 0.990** 3.782
22 Y 0.876 3.453
26 A 0.866 3.425
36 T 0.908 3.544
51 E 0.994** 3.793
54 C 1.000** 3.810
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: S25_SFBB1)
Pr(w>1) post mean +- SE for w
7 Q 0.922 3.405 +- 1.110
19 Q 0.993** 3.628 +- 0.909
20 Y 0.561 2.261 +- 1.383
22 Y 0.908 3.314 +- 1.075
26 A 0.898 3.282 +- 1.098
36 T 0.931 3.408 +- 1.053
37 T 0.603 2.337 +- 1.287
51 E 0.995** 3.629 +- 0.893
54 C 1.000** 3.646 +- 0.885
