--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Nov 08 14:39:07 WET 2017
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=
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/afazer/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/afazer/S24_16SFBBs/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/afazer/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -7220.69 -7242.17
2 -7221.07 -7241.03
--------------------------------------
TOTAL -7220.87 -7241.76
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/afazer/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/afazer/S24_16SFBBs/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/afazer/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.468552 0.003813 1.352008 1.591112 1.467593 1446.42 1473.71 1.000
r(A<->C){all} 0.122725 0.000150 0.100130 0.147025 0.122558 993.25 1048.60 1.000
r(A<->G){all} 0.301677 0.000343 0.266289 0.339055 0.301739 1024.17 1025.93 1.000
r(A<->T){all} 0.076277 0.000065 0.061683 0.092616 0.075751 978.38 984.05 1.000
r(C<->G){all} 0.147574 0.000240 0.117182 0.178490 0.147331 710.60 769.15 1.003
r(C<->T){all} 0.264095 0.000305 0.231951 0.300486 0.263543 706.23 745.04 1.000
r(G<->T){all} 0.087652 0.000092 0.069672 0.107478 0.087225 916.49 1028.76 1.000
pi(A){all} 0.294814 0.000118 0.274994 0.317496 0.294622 916.51 957.14 1.001
pi(C){all} 0.174971 0.000073 0.159079 0.191901 0.174700 838.09 1035.25 1.000
pi(G){all} 0.197531 0.000091 0.180069 0.216654 0.197468 1062.42 1105.09 1.002
pi(T){all} 0.332683 0.000129 0.310092 0.353711 0.332581 794.04 945.68 1.000
alpha{1,2} 0.751182 0.013573 0.548740 0.985164 0.735424 1161.86 1311.14 1.000
alpha{3} 2.225203 0.357829 1.203322 3.384510 2.128764 1374.50 1407.12 1.000
pinvar{all} 0.049795 0.001356 0.000007 0.121174 0.042494 1311.58 1319.49 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 -5215.795623
Model 2: PositiveSelection -5188.452727
Model 0: one-ratio -5337.455602
Model 3: discrete -5188.061232
Model 7: beta -5225.672714
Model 8: beta&w>1 -5188.441373
Model 0 vs 1 243.31995800000004
Model 2 vs 1 54.68579200000022
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S24_SFBB1)
Pr(w>1) post mean +- SE for w
14 N 0.992** 3.160
20 R 0.999** 3.175
24 P 0.972* 3.117
53 L 0.958* 3.086
60 E 0.928 3.021
72 L 0.719 2.565
101 R 0.752 2.636
108 I 0.996** 3.168
110 T 0.998** 3.173
127 Q 0.856 2.864
139 Q 0.502 2.093
156 T 0.580 2.262
171 E 0.957* 3.084
174 C 0.884 2.924
190 T 0.998** 3.173
192 E 0.839 2.826
220 K 0.599 2.305
240 P 0.805 2.753
241 D 0.958* 3.085
242 E 0.873 2.901
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: S24_SFBB1)
Pr(w>1) post mean +- SE for w
14 N 0.990** 3.237 +- 0.529
20 R 0.999** 3.257 +- 0.488
24 P 0.966* 3.179 +- 0.626
53 L 0.951* 3.143 +- 0.679
60 E 0.919 3.072 +- 0.770
72 L 0.670 2.458 +- 1.102
101 R 0.708 2.553 +- 1.081
108 I 0.995** 3.249 +- 0.506
110 T 0.998** 3.255 +- 0.494
127 Q 0.837 2.875 +- 0.941
156 T 0.542 2.164 +- 1.135
171 E 0.946 3.128 +- 0.694
174 C 0.864 2.935 +- 0.892
190 T 0.998** 3.254 +- 0.494
192 E 0.809 2.800 +- 0.979
220 K 0.551 2.175 +- 1.125
240 P 0.771 2.708 +- 1.026
241 D 0.948 3.136 +- 0.686
242 E 0.846 2.887 +- 0.922
Model 8 vs 7 74.46268200000122
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S24_SFBB1)
Pr(w>1) post mean +- SE for w
14 N 0.998** 2.733
20 R 1.000** 2.737
24 P 0.992** 2.722
53 L 0.985* 2.710
58 F 0.759 2.285
60 E 0.970* 2.682
62 G 0.516 1.809
72 L 0.896 2.543
73 A 0.621 2.014
85 G 0.506 1.774
101 R 0.904 2.557
108 I 0.998** 2.735
110 T 0.999** 2.736
127 Q 0.935 2.614
139 Q 0.712 2.184
142 Y 0.709 2.190
156 T 0.780 2.317
171 E 0.988* 2.715
174 C 0.956* 2.656
190 T 0.999** 2.736
192 E 0.937 2.619
220 K 0.826 2.410
237 C 0.760 2.288
240 P 0.924 2.595
241 D 0.988* 2.715
242 E 0.958* 2.660
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: S24_SFBB1)
Pr(w>1) post mean +- SE for w
1 L 0.509 1.643 +- 0.890
14 N 0.998** 2.517 +- 0.154
20 R 1.000** 2.519 +- 0.142
24 P 0.994** 2.509 +- 0.186
53 L 0.989* 2.501 +- 0.218
58 F 0.855 2.268 +- 0.594
60 E 0.978* 2.482 +- 0.281
62 G 0.662 1.928 +- 0.818
72 L 0.933 2.403 +- 0.434
73 A 0.746 2.075 +- 0.750
85 G 0.629 1.859 +- 0.855
101 R 0.937 2.410 +- 0.425
108 I 0.999** 2.517 +- 0.151
110 T 0.999** 2.518 +- 0.145
127 Q 0.952* 2.437 +- 0.384
138 E 0.598 1.817 +- 0.848
139 Q 0.798 2.163 +- 0.701
142 Y 0.822 2.211 +- 0.647
156 T 0.848 2.253 +- 0.626
171 E 0.992** 2.505 +- 0.203
174 C 0.970* 2.467 +- 0.316
190 T 0.999** 2.518 +- 0.146
192 E 0.957* 2.444 +- 0.366
220 K 0.888 2.324 +- 0.542
231 I 0.562 1.753 +- 0.860
237 C 0.860 2.276 +- 0.583
240 P 0.949 2.430 +- 0.392
241 D 0.992** 2.506 +- 0.201
242 E 0.972* 2.472 +- 0.302
