--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Dec 11 16:16:33 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/pet1/Phyb_S11_16/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Phyb_S11_16/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/pet1/Phyb_S11_16/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -13379.35 -13397.56
2 -13379.19 -13397.93
--------------------------------------
TOTAL -13379.27 -13397.76
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/pet1/Phyb_S11_16/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Phyb_S11_16/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/pet1/Phyb_S11_16/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 3.494552 0.013028 3.279636 3.710562 3.493504 1182.30 1341.65 1.001
r(A<->C){all} 0.125183 0.000087 0.106094 0.142393 0.125303 997.19 1033.52 1.001
r(A<->G){all} 0.282405 0.000208 0.252593 0.307832 0.282318 663.55 671.84 1.000
r(A<->T){all} 0.099103 0.000046 0.086272 0.112745 0.098928 829.51 878.30 1.000
r(C<->G){all} 0.140886 0.000127 0.119832 0.164050 0.140743 702.80 806.82 1.001
r(C<->T){all} 0.271781 0.000196 0.246102 0.299765 0.271434 622.21 629.66 1.001
r(G<->T){all} 0.080642 0.000051 0.066717 0.094182 0.080602 993.96 1010.34 1.000
pi(A){all} 0.312466 0.000091 0.292173 0.329767 0.312422 801.31 924.42 1.000
pi(C){all} 0.173854 0.000054 0.159400 0.187846 0.173705 698.51 740.28 1.000
pi(G){all} 0.189555 0.000063 0.174019 0.205005 0.189315 936.17 951.27 1.000
pi(T){all} 0.324125 0.000100 0.304281 0.343619 0.324297 880.12 920.04 1.000
alpha{1,2} 1.292747 0.024102 0.994012 1.589009 1.281398 1164.66 1196.45 1.000
alpha{3} 4.549691 0.863548 2.882597 6.365786 4.469673 1233.44 1367.22 1.001
pinvar{all} 0.058902 0.000405 0.021599 0.101743 0.059364 1218.79 1224.81 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 -11935.751585
Model 2: PositiveSelection -11931.332441
Model 0: one-ratio -12126.169794
Model 3: discrete -11875.402594
Model 7: beta -11892.978867
Model 8: beta&w>1 -11877.130821
Model 0 vs 1 380.83641799999896
Model 2 vs 1 8.838287999999011
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 1_Phybrida_S11_SLF10_AB933018)
Pr(w>1) post mean +- SE for w
51 F 0.853 2.049
65 Y 0.879 2.080
67 F 0.632 1.777
119 L 0.874 2.075
150 S 0.585 1.719
201 W 0.791 1.972
218 A 0.809 1.995
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: 1_Phybrida_S11_SLF10_AB933018)
Pr(w>1) post mean +- SE for w
51 F 0.877 2.230 +- 0.554
65 Y 0.899 2.268 +- 0.522
67 F 0.666 1.923 +- 0.709
119 L 0.895 2.258 +- 0.529
150 S 0.623 1.863 +- 0.722
201 W 0.817 2.142 +- 0.616
218 A 0.838 2.174 +- 0.597
Model 8 vs 7 31.696091999998316
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 1_Phybrida_S11_SLF10_AB933018)
Pr(w>1) post mean +- SE for w
48 T 0.642 1.337
51 F 0.982* 1.655
65 Y 0.975* 1.648
67 F 0.952* 1.628
98 A 0.865 1.549
101 I 0.554 1.255
119 L 0.982* 1.656
150 S 0.945 1.622
173 K 0.747 1.438
176 D 0.514 1.210
179 M 0.803 1.490
198 F 0.813 1.499
201 W 0.976* 1.649
202 F 0.700 1.392
217 F 0.793 1.483
218 A 0.977* 1.651
265 S 0.826 1.512
315 H 0.570 1.274
336 E 0.739 1.433
349 A 0.814 1.500
358 E 0.813 1.500
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: 1_Phybrida_S11_SLF10_AB933018)
Pr(w>1) post mean +- SE for w
48 T 0.536 1.170 +- 0.390
51 F 0.945 1.484 +- 0.207
65 Y 0.928 1.471 +- 0.227
67 F 0.893 1.447 +- 0.250
98 A 0.770 1.357 +- 0.321
119 L 0.946 1.485 +- 0.206
150 S 0.880 1.438 +- 0.259
173 K 0.641 1.253 +- 0.367
179 M 0.698 1.297 +- 0.355
198 F 0.703 1.304 +- 0.358
201 W 0.934 1.476 +- 0.217
202 F 0.582 1.208 +- 0.388
217 F 0.688 1.295 +- 0.352
218 A 0.937 1.478 +- 0.215
265 S 0.723 1.319 +- 0.345
336 E 0.641 1.256 +- 0.355
349 A 0.706 1.304 +- 0.357
358 E 0.712 1.309 +- 0.345
