--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Dec 07 19:29:07 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/408/Sur-8-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/408/Sur-8-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/408/Sur-8-PA/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/408/Sur-8-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -7086.88 -7103.64
2 -7086.89 -7102.84
--------------------------------------
TOTAL -7086.88 -7103.31
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/408/Sur-8-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/408/Sur-8-PA/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/408/Sur-8-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.195491 0.005079 1.064296 1.342105 1.193626 1277.79 1389.39 1.000
r(A<->C){all} 0.086150 0.000145 0.062349 0.109473 0.085834 723.27 875.01 1.000
r(A<->G){all} 0.231192 0.000430 0.186599 0.269271 0.231086 621.98 716.35 1.000
r(A<->T){all} 0.140227 0.000371 0.102731 0.176604 0.139750 729.80 791.61 1.000
r(C<->G){all} 0.047511 0.000049 0.034876 0.061441 0.047311 1101.71 1159.58 1.000
r(C<->T){all} 0.446736 0.000745 0.394032 0.501646 0.446119 795.43 862.46 1.000
r(G<->T){all} 0.048184 0.000093 0.029111 0.065893 0.047844 872.03 1113.43 1.000
pi(A){all} 0.237959 0.000085 0.220477 0.256198 0.237927 1019.93 1109.49 1.000
pi(C){all} 0.289033 0.000090 0.270218 0.306483 0.288774 953.35 1060.16 1.000
pi(G){all} 0.284400 0.000089 0.266388 0.303524 0.284420 1080.67 1172.01 1.000
pi(T){all} 0.188608 0.000062 0.174040 0.204384 0.188407 1112.96 1138.34 1.000
alpha{1,2} 0.146606 0.000139 0.124091 0.169705 0.146083 1266.42 1337.70 1.000
alpha{3} 4.122839 0.885541 2.367195 5.906466 4.033102 1289.17 1306.11 1.000
pinvar{all} 0.340675 0.000925 0.274959 0.396201 0.341613 1269.76 1339.72 1.001
------------------------------------------------------------------------------------------------------
* 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 -6163.564101
Model 2: PositiveSelection -6163.564119
Model 0: one-ratio -6268.228403
Model 3: discrete -6157.426672
Model 7: beta -6166.924836
Model 8: beta&w>1 -6157.495092
Model 0 vs 1 209.32860400000027
Model 2 vs 1 3.5999999454361387E-5
Model 8 vs 7 18.859488000000056
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Sur-8-PA)
Pr(w>1) post mean +- SE for w
38 S 0.751 0.785
42 T 0.999** 1.005
43 S 0.964* 0.974
44 A 0.852 0.875
47 P 0.973* 0.982
53 G 0.808 0.836
54 S 0.984* 0.992
56 T 0.746 0.781
61 A 0.997** 1.003
62 G 0.592 0.644
63 T 0.578 0.632
67 S 0.979* 0.987
69 A 0.792 0.822
70 N 0.996** 1.003
71 G 0.994** 1.001
72 S 0.998** 1.005
85 L 0.973* 0.982
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_Sur-8-PA)
Pr(w>1) post mean +- SE for w
42 T 0.894 1.412 +- 0.275
47 P 0.783 1.293 +- 0.414
54 S 0.671 1.190 +- 0.460
61 A 0.774 1.300 +- 0.386
67 S 0.602 1.120 +- 0.486
70 N 0.761 1.286 +- 0.398
71 G 0.805 1.326 +- 0.370
72 S 0.915 1.430 +- 0.250
85 L 0.782 1.292 +- 0.414
