--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Nov 04 00:04:11 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/revmuscle/S3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S3/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/revmuscle/S3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -8327.87 -8351.75
2 -8328.34 -8344.29
--------------------------------------
TOTAL -8328.08 -8351.06
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/revmuscle/S3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S3/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/revmuscle/S3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.431429 0.003269 1.328174 1.548621 1.428802 1440.28 1466.47 1.000
r(A<->C){all} 0.121802 0.000131 0.100595 0.145077 0.121209 973.83 1047.10 1.000
r(A<->G){all} 0.301159 0.000317 0.267862 0.335866 0.300692 696.70 755.82 1.000
r(A<->T){all} 0.073501 0.000049 0.060267 0.087187 0.073222 929.09 1051.96 1.000
r(C<->G){all} 0.145617 0.000216 0.118516 0.174942 0.145172 680.00 756.64 1.000
r(C<->T){all} 0.281753 0.000277 0.249187 0.314793 0.281507 710.14 779.89 1.000
r(G<->T){all} 0.076169 0.000066 0.060722 0.093006 0.075893 1072.26 1072.28 1.000
pi(A){all} 0.298673 0.000106 0.277637 0.317205 0.298567 959.65 977.51 1.000
pi(C){all} 0.163286 0.000068 0.148698 0.180744 0.163242 790.87 904.58 1.000
pi(G){all} 0.190629 0.000077 0.174534 0.208469 0.190326 952.68 1011.53 1.000
pi(T){all} 0.347412 0.000123 0.326188 0.369551 0.347509 873.55 912.57 1.000
alpha{1,2} 0.839632 0.012965 0.648221 1.075981 0.825289 1233.92 1304.91 1.001
alpha{3} 1.628894 0.115782 1.068621 2.317282 1.586078 1372.95 1421.04 1.001
pinvar{all} 0.033667 0.000788 0.000029 0.088961 0.026467 1004.18 1126.94 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 -5672.221451
Model 2: PositiveSelection -5630.921412
Model 0: one-ratio -5794.279507
Model 3: discrete -5630.463639
Model 7: beta -5677.10328
Model 8: beta&w>1 -5630.345892
Model 0 vs 1 244.1161119999997
Model 2 vs 1 82.6000780000013
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S3_SFBB1)
Pr(w>1) post mean +- SE for w
42 N 0.987* 4.451
48 R 1.000** 4.494
52 P 0.954* 4.334
81 L 0.938 4.278
88 E 0.988* 4.453
129 R 0.877 4.063
137 I 1.000** 4.494
139 T 0.999** 4.490
156 Q 0.729 3.547
185 T 0.597 3.086
203 C 0.927 4.238
219 T 1.000** 4.494
221 E 0.995** 4.478
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: S3_SFBB1)
Pr(w>1) post mean +- SE for w
42 N 0.983* 4.552 +- 0.734
48 R 1.000** 4.617 +- 0.572
52 P 0.939 4.387 +- 1.019
81 L 0.918 4.306 +- 1.124
88 E 0.986* 4.569 +- 0.707
129 R 0.839 4.003 +- 1.408
137 I 1.000** 4.618 +- 0.571
139 T 0.999** 4.613 +- 0.586
156 Q 0.692 3.482 +- 1.720
185 T 0.544 2.910 +- 1.793
203 C 0.903 4.250 +- 1.188
219 T 1.000** 4.618 +- 0.570
221 E 0.994** 4.597 +- 0.631
Model 8 vs 7 93.51477599999998
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S3_SFBB1)
Pr(w>1) post mean +- SE for w
42 N 0.994** 3.951
48 R 1.000** 3.969
52 P 0.976* 3.897
81 L 0.966* 3.865
88 E 0.992** 3.945
129 R 0.934 3.769
137 I 1.000** 3.969
139 T 0.999** 3.967
156 Q 0.804 3.364
185 T 0.736 3.156
203 C 0.962* 3.852
219 T 1.000** 3.969
221 E 0.997** 3.961
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: S3_SFBB1)
Pr(w>1) post mean +- SE for w
42 N 0.992** 4.077 +- 0.618
48 R 1.000** 4.103 +- 0.556
52 P 0.971* 4.006 +- 0.766
81 L 0.957* 3.961 +- 0.842
88 E 0.991** 4.075 +- 0.629
129 R 0.916 3.819 +- 1.029
137 I 1.000** 4.103 +- 0.555
139 T 0.999** 4.100 +- 0.562
156 Q 0.777 3.374 +- 1.428
185 T 0.685 3.050 +- 1.535
203 C 0.952* 3.942 +- 0.870
219 T 1.000** 4.103 +- 0.555
221 E 0.997** 4.093 +- 0.581
