--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Jan 21 23:14:25 GMT 2019
codeml.models=7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=/usr/bin/
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb
tcoffee.bin=t_coffee
mrbayes.dir=/opt/mrbayes_3.2.2/src
tcoffee.dir=
tcoffee.minScore=3
input.fasta=
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/data/ENV/ENV/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/ENV/ENV/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
(Use the harmonic mean for Bayes factor comparisons of models)
(Values are saved to the file /data/ENV/ENV/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -89950.80 -90023.48
2 -89946.84 -90013.59
--------------------------------------
TOTAL -89947.51 -90022.78
--------------------------------------
Model parameter summaries over the runs sampled in files
"/data/ENV/ENV/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/ENV/ENV/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 "/data/ENV/ENV/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 22.358251 0.467479 21.038360 23.736390 22.362520 228.04 236.16 1.031
r(A<->C){all} 0.133319 0.000014 0.126100 0.140897 0.133272 132.42 184.67 1.000
r(A<->G){all} 0.292938 0.000100 0.273221 0.311567 0.293620 43.24 55.29 1.020
r(A<->T){all} 0.056715 0.000006 0.052108 0.061414 0.056721 241.02 306.60 1.000
r(C<->G){all} 0.067239 0.000011 0.061059 0.074207 0.067122 251.39 355.75 1.001
r(C<->T){all} 0.355171 0.000116 0.333621 0.375352 0.354121 42.62 57.46 1.016
r(G<->T){all} 0.094619 0.000013 0.087328 0.101647 0.094563 246.23 271.86 1.000
pi(A){all} 0.401069 0.000030 0.390225 0.411562 0.401041 147.59 153.90 1.019
pi(C){all} 0.172329 0.000017 0.164333 0.180116 0.172418 102.59 104.11 1.015
pi(G){all} 0.220128 0.000022 0.211291 0.229645 0.220055 113.61 126.32 1.004
pi(T){all} 0.206474 0.000025 0.197563 0.217194 0.206422 94.27 101.21 1.013
alpha{1,2} 0.599388 0.000202 0.571370 0.626880 0.599160 1142.06 1214.82 1.000
alpha{3} 0.824767 0.000893 0.762167 0.880046 0.823922 1042.24 1188.62 1.006
pinvar{all} 0.178981 0.000082 0.160956 0.196335 0.179227 904.41 977.04 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 7: beta -70964.774764
Model 8: beta&w>1 -69895.444709
Model 8 vs 7 2138.660109999997
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: B.NL.87.19298_9E8.GU455480_)
Pr(w>1) post mean +- SE for w
5 R 1.000** 2.996
8 T 0.994** 2.984
67 V 1.000** 2.996
111 T 1.000** 2.996
121 I 1.000** 2.996
128 V 0.927 2.848
131 Y 0.925 2.844
137 L 0.839 2.668
143 D 1.000** 2.996
144 N 1.000** 2.996
145 D 1.000** 2.996
155 V 0.996** 2.988
187 K 0.618 2.218
195 K 0.764 2.517
235 A 1.000** 2.996
237 T 0.504 1.986
245 T 1.000** 2.996
247 E 1.000** 2.996
254 N 1.000** 2.996
269 E 1.000** 2.996
283 I 1.000** 2.996
284 T 1.000** 2.996
285 K 1.000** 2.996
288 N 1.000** 2.996
291 Q 1.000** 2.996
292 Q 1.000** 2.996
294 V 1.000** 2.996
295 E 1.000** 2.996
298 R 1.000** 2.996
305 E 1.000** 2.996
307 K 1.000** 2.996
308 S 1.000** 2.996
333 K 1.000** 2.996
337 S 0.949 2.894
338 S 1.000** 2.996
339 T 1.000** 2.996
340 E 1.000** 2.996
341 R 1.000** 2.996
369 K 1.000** 2.996
371 Q 1.000** 2.996
375 V 1.000** 2.996
389 T 1.000** 2.996
390 D 1.000** 2.996
391 T 1.000** 2.996
426 R 1.000** 2.996
530 A 1.000** 2.996
535 A 1.000** 2.996
541 S 0.604 2.188
542 L 1.000** 2.996
543 N 1.000** 2.996
544 E 1.000** 2.996
547 D 1.000** 2.996
559 E 1.000** 2.996
563 G 1.000** 2.996
567 N 1.000** 2.996
571 K 0.954* 2.903
597 S 1.000** 2.996
643 R 0.982* 2.960
644 H 1.000** 2.996
646 G 1.000** 2.996
647 P 0.984* 2.963
669 D 1.000** 2.996
673 N 0.828 2.647
679 F 1.000** 2.996
693 R 0.987* 2.969
705 A 1.000** 2.996
714 Q 0.886 2.764
745 V 0.595 2.172
749 I 0.999** 2.995
750 Y 1.000** 2.996
754 I 1.000** 2.996
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: B.NL.87.19298_9E8.GU455480_)
Pr(w>1) post mean +- SE for w
5 R 1.000** 2.829 +- 0.471
8 T 0.968* 2.748 +- 0.560
44 D 0.591 1.862 +- 0.767
67 V 1.000** 2.829 +- 0.470
111 T 1.000** 2.829 +- 0.470
112 D 0.664 1.980 +- 0.738
121 I 1.000** 2.829 +- 0.470
128 V 0.735 2.154 +- 0.765
131 Y 0.773 2.250 +- 0.771
137 L 0.723 2.125 +- 0.771
143 D 1.000** 2.829 +- 0.470
144 N 1.000** 2.829 +- 0.470
145 D 1.000** 2.829 +- 0.470
155 V 0.986* 2.794 +- 0.513
164 S 0.594 1.866 +- 0.783
187 K 0.673 2.000 +- 0.742
195 K 0.687 2.033 +- 0.748
233 D 0.649 1.955 +- 0.748
235 A 1.000** 2.829 +- 0.470
237 T 0.664 1.983 +- 0.747
245 T 1.000** 2.828 +- 0.471
247 E 1.000** 2.829 +- 0.470
249 N 0.649 1.954 +- 0.747
254 N 1.000** 2.829 +- 0.470
269 E 1.000** 2.829 +- 0.470
276 Q 0.587 1.855 +- 0.771
283 I 1.000** 2.829 +- 0.470
284 T 1.000** 2.829 +- 0.470
285 K 1.000** 2.829 +- 0.470
288 N 1.000** 2.829 +- 0.470
291 Q 1.000** 2.829 +- 0.470
292 Q 1.000** 2.829 +- 0.470
294 V 1.000** 2.829 +- 0.470
295 E 1.000** 2.829 +- 0.470
298 R 1.000** 2.829 +- 0.470
305 E 1.000** 2.829 +- 0.470
307 K 1.000** 2.829 +- 0.470
308 S 1.000** 2.829 +- 0.470
333 K 1.000** 2.829 +- 0.470
337 S 0.747 2.184 +- 0.767
338 S 1.000** 2.829 +- 0.470
339 T 1.000** 2.829 +- 0.470
340 E 1.000** 2.829 +- 0.470
341 R 1.000** 2.829 +- 0.470
369 K 1.000** 2.829 +- 0.470
371 Q 1.000** 2.829 +- 0.470
373 S 0.655 1.963 +- 0.742
375 V 1.000** 2.829 +- 0.470
389 T 1.000** 2.829 +- 0.470
390 D 1.000** 2.829 +- 0.470
391 T 1.000** 2.829 +- 0.470
426 R 1.000** 2.829 +- 0.470
530 A 1.000** 2.829 +- 0.470
535 A 1.000** 2.829 +- 0.471
541 S 0.672 2.004 +- 0.757
542 L 1.000** 2.829 +- 0.470
543 N 1.000** 2.829 +- 0.470
544 E 1.000** 2.829 +- 0.470
547 D 1.000** 2.829 +- 0.470
559 E 1.000** 2.829 +- 0.471
563 G 1.000** 2.829 +- 0.470
567 N 1.000** 2.829 +- 0.470
571 K 0.751 2.195 +- 0.767
597 S 1.000** 2.829 +- 0.470
600 N 0.638 1.936 +- 0.750
643 R 0.936 2.665 +- 0.629
644 H 1.000** 2.829 +- 0.470
646 G 1.000** 2.829 +- 0.470
647 P 0.952* 2.708 +- 0.597
669 D 1.000** 2.829 +- 0.471
673 N 0.697 2.058 +- 0.754
679 F 1.000** 2.829 +- 0.470
693 R 0.968* 2.748 +- 0.562
705 A 1.000** 2.829 +- 0.471
714 Q 0.795 2.311 +- 0.774
745 V 0.673 1.999 +- 0.743
746 L 0.562 1.817 +- 0.774
749 I 0.997** 2.822 +- 0.479
750 Y 1.000** 2.829 +- 0.470
754 I 1.000** 2.829 +- 0.470
764 L 0.584 1.849 +- 0.777
