--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Dec 11 15:24:28 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/Paxi_S17_18/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Paxi_S17_18/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/Paxi_S17_18/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -13005.99 -13029.65
2 -13005.19 -13025.43
--------------------------------------
TOTAL -13005.51 -13028.97
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/pet1/Paxi_S17_18/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Paxi_S17_18/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/Paxi_S17_18/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 3.314020 0.012177 3.107430 3.541277 3.311933 1319.42 1392.99 1.000
r(A<->C){all} 0.129913 0.000097 0.111178 0.149571 0.129551 815.21 836.13 1.000
r(A<->G){all} 0.289550 0.000221 0.261340 0.318448 0.289720 545.21 632.33 1.001
r(A<->T){all} 0.093685 0.000046 0.080302 0.106540 0.093540 743.47 855.97 1.000
r(C<->G){all} 0.144108 0.000136 0.120699 0.167158 0.143902 939.61 984.42 1.000
r(C<->T){all} 0.264744 0.000192 0.240379 0.293945 0.264537 689.11 776.35 1.001
r(G<->T){all} 0.078000 0.000050 0.064308 0.091748 0.077955 742.97 901.38 1.000
pi(A){all} 0.306409 0.000097 0.287048 0.325395 0.306474 766.93 876.17 1.000
pi(C){all} 0.173127 0.000056 0.158969 0.188238 0.173137 600.30 652.91 1.000
pi(G){all} 0.188620 0.000062 0.173871 0.204199 0.188553 813.11 883.35 1.000
pi(T){all} 0.331844 0.000099 0.312849 0.351501 0.331612 879.41 927.65 1.000
alpha{1,2} 1.365841 0.033435 1.044485 1.740269 1.345293 1062.28 1200.18 1.000
alpha{3} 4.358836 0.778390 2.806055 6.140304 4.266587 1343.27 1422.13 1.000
pinvar{all} 0.073339 0.000450 0.030123 0.112874 0.073448 969.40 1117.08 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 -9431.533536
Model 2: PositiveSelection -9425.946372
Model 0: one-ratio -9601.348048
Model 3: discrete -9388.374123
Model 7: beta -9407.071555
Model 8: beta&w>1 -9388.402901
Model 0 vs 1 339.629023999998
Model 2 vs 1 11.174328000000969
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_Paxillaris_S17_SLF10_AB933031)
Pr(w>1) post mean +- SE for w
2 Y 0.760 1.948
4 F 0.895 2.117
35 A 0.589 1.734
55 S 0.893 2.115
56 L 0.893 2.114
136 F 0.838 2.046
139 W 0.551 1.688
155 F 0.681 1.850
156 V 0.827 2.031
272 E 0.679 1.848
285 A 0.685 1.855
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_Paxillaris_S17_SLF10_AB933031)
Pr(w>1) post mean +- SE for w
2 Y 0.759 2.122 +- 0.660
4 F 0.890 2.315 +- 0.506
35 A 0.555 1.815 +- 0.748
55 S 0.897 2.328 +- 0.494
56 L 0.895 2.324 +- 0.498
136 F 0.843 2.248 +- 0.573
155 F 0.661 1.973 +- 0.720
156 V 0.832 2.232 +- 0.587
272 E 0.655 1.963 +- 0.722
285 A 0.653 1.959 +- 0.721
Model 8 vs 7 37.33730800000194
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_Paxillaris_S17_SLF10_AB933031)
Pr(w>1) post mean +- SE for w
2 Y 0.952* 1.678
4 F 0.989* 1.716
35 A 0.940 1.667
38 I 0.615 1.336
55 S 0.986* 1.712
56 L 0.987* 1.713
85 S 0.800 1.524
87 S 0.762 1.487
97 A 0.561 1.275
114 D 0.885 1.611
117 M 0.824 1.548
136 F 0.973* 1.699
139 W 0.925 1.651
140 F 0.849 1.574
155 F 0.955* 1.681
156 V 0.972* 1.698
199 P 0.853 1.579
272 E 0.957* 1.684
285 A 0.956* 1.683
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_Paxillaris_S17_SLF10_AB933031)
Pr(w>1) post mean +- SE for w
2 Y 0.868 1.677 +- 0.549
4 F 0.955* 1.756 +- 0.489
35 A 0.830 1.627 +- 0.552
55 S 0.947 1.752 +- 0.497
56 L 0.949 1.753 +- 0.495
85 S 0.591 1.342 +- 0.573
87 S 0.523 1.250 +- 0.522
114 D 0.729 1.513 +- 0.583
117 M 0.617 1.369 +- 0.570
136 F 0.914 1.722 +- 0.520
139 W 0.786 1.567 +- 0.560
140 F 0.656 1.416 +- 0.575
155 F 0.865 1.667 +- 0.541
156 V 0.911 1.720 +- 0.522
199 P 0.675 1.449 +- 0.586
272 E 0.870 1.671 +- 0.538
285 A 0.867 1.666 +- 0.540
