--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Nov 10 18:46:50 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/191/CG8312-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/191/CG8312-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/191/CG8312-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/191/CG8312-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -9105.76 -9126.01
2 -9105.91 -9125.76
--------------------------------------
TOTAL -9105.83 -9125.89
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/191/CG8312-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/191/CG8312-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/191/CG8312-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} 0.797308 0.001733 0.715572 0.877058 0.796028 1245.63 1373.32 1.000
r(A<->C){all} 0.085027 0.000102 0.065567 0.104218 0.084534 927.09 999.24 1.000
r(A<->G){all} 0.191224 0.000271 0.159482 0.223138 0.190815 748.12 809.51 1.000
r(A<->T){all} 0.106758 0.000256 0.076000 0.138981 0.106150 742.72 834.22 1.000
r(C<->G){all} 0.071431 0.000057 0.057510 0.086402 0.071185 949.61 1071.21 1.000
r(C<->T){all} 0.453254 0.000543 0.408258 0.498942 0.453114 674.83 729.80 1.000
r(G<->T){all} 0.092306 0.000137 0.071058 0.115565 0.091863 1055.36 1139.35 1.001
pi(A){all} 0.243624 0.000062 0.228348 0.259040 0.243516 1013.37 1097.30 1.000
pi(C){all} 0.298177 0.000063 0.282092 0.312819 0.298346 1030.66 1075.34 1.000
pi(G){all} 0.308598 0.000069 0.291241 0.323689 0.308632 1075.68 1105.99 1.000
pi(T){all} 0.149601 0.000038 0.137858 0.161733 0.149385 901.22 911.77 1.000
alpha{1,2} 0.164519 0.000231 0.135573 0.194509 0.164507 1279.15 1336.09 1.000
alpha{3} 4.088486 1.000038 2.261959 6.037891 3.953266 985.55 1157.79 1.003
pinvar{all} 0.326374 0.001165 0.259287 0.391647 0.328481 1079.13 1193.32 1.002
------------------------------------------------------------------------------------------------------
* 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 -7985.933295
Model 2: PositiveSelection -7985.933295
Model 0: one-ratio -8098.578686
Model 3: discrete -7960.665157
Model 7: beta -7967.58304
Model 8: beta&w>1 -7961.029397
Model 0 vs 1 225.29078200000004
Model 2 vs 1 0.0
Model 8 vs 7 13.107286000000386
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_CG8312-PA)
Pr(w>1) post mean +- SE for w
9 S 0.919 1.616
13 D 0.996** 1.723
48 V 0.752 1.383
93 A 0.924 1.624
588 T 0.767 1.406
668 A 0.940 1.646
832 T 0.596 1.168
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_CG8312-PA)
Pr(w>1) post mean +- SE for w
9 S 0.933 1.447 +- 0.231
13 D 0.981* 1.490 +- 0.126
48 V 0.867 1.380 +- 0.335
52 A 0.622 1.090 +- 0.557
93 A 0.929 1.445 +- 0.232
96 T 0.681 1.183 +- 0.489
97 T 0.595 1.091 +- 0.520
98 A 0.629 1.129 +- 0.507
484 S 0.667 1.187 +- 0.463
588 T 0.853 1.376 +- 0.323
635 T 0.531 1.042 +- 0.510
668 A 0.927 1.444 +- 0.229
832 T 0.778 1.304 +- 0.387
833 S 0.728 1.214 +- 0.498
