--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Nov 04 00:51:58 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/S5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S5/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/S5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -7424.07 -7444.15
2 -7424.04 -7441.68
--------------------------------------
TOTAL -7424.05 -7443.54
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/revmuscle/S5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S5/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/S5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.426375 0.003662 1.306126 1.543630 1.423657 1383.30 1414.01 1.000
r(A<->C){all} 0.107254 0.000134 0.084813 0.129427 0.107064 980.02 1043.24 1.000
r(A<->G){all} 0.323886 0.000373 0.287849 0.363455 0.323110 604.51 637.98 1.000
r(A<->T){all} 0.078767 0.000061 0.063585 0.093697 0.078639 1035.32 1037.82 1.000
r(C<->G){all} 0.138346 0.000213 0.110366 0.167488 0.137772 984.30 1054.38 1.000
r(C<->T){all} 0.270755 0.000301 0.236655 0.304718 0.270668 880.28 918.88 1.001
r(G<->T){all} 0.080992 0.000084 0.063736 0.098878 0.080549 1102.07 1132.03 1.000
pi(A){all} 0.292442 0.000112 0.271284 0.312944 0.292706 1043.16 1198.88 1.000
pi(C){all} 0.174849 0.000078 0.158255 0.192544 0.174745 980.85 1078.25 1.000
pi(G){all} 0.195289 0.000081 0.178568 0.213335 0.195274 991.53 1051.25 1.000
pi(T){all} 0.337420 0.000127 0.316082 0.359862 0.337484 1115.48 1172.99 1.000
alpha{1,2} 0.883018 0.025913 0.611356 1.205751 0.855502 935.91 1093.07 1.000
alpha{3} 1.509877 0.160454 0.867752 2.316765 1.435413 903.97 1051.19 1.000
pinvar{all} 0.060048 0.001930 0.000026 0.142941 0.051618 1027.63 1084.58 1.001
------------------------------------------------------------------------------------------------------
* 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 -3649.488118
Model 2: PositiveSelection -3625.008556
Model 0: one-ratio -3727.832062
Model 3: discrete -3622.128473
Model 7: beta -3648.567478
Model 8: beta&w>1 -3621.601279
Model 0 vs 1 156.68788799999948
Model 2 vs 1 48.959123999999974
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S5_SFBB1)
Pr(w>1) post mean +- SE for w
8 L 0.593 2.778
36 R 0.872 3.616
44 I 0.999** 3.996
46 T 1.000** 3.997
63 Q 0.845 3.533
75 Q 0.566 2.697
78 Y 0.709 3.125
107 E 0.998** 3.991
110 C 0.955* 3.863
126 T 1.000** 3.998
128 E 0.969* 3.905
156 K 0.705 3.114
176 P 0.761 3.283
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: S5_SFBB1)
Pr(w>1) post mean +- SE for w
8 L 0.513 2.543 +- 1.562
36 R 0.824 3.594 +- 1.331
44 I 0.999** 4.201 +- 0.684
46 T 0.999** 4.203 +- 0.680
63 Q 0.812 3.580 +- 1.377
75 Q 0.505 2.550 +- 1.596
78 Y 0.636 2.955 +- 1.558
107 E 0.997** 4.194 +- 0.699
110 C 0.941 4.004 +- 0.994
126 T 1.000** 4.204 +- 0.677
128 E 0.960* 4.070 +- 0.910
156 K 0.630 2.939 +- 1.563
176 P 0.705 3.207 +- 1.524
Model 8 vs 7 53.93239799999992
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S5_SFBB1)
Pr(w>1) post mean +- SE for w
8 L 0.730 2.730
21 G 0.620 2.447
36 R 0.916 3.192
44 I 0.999** 3.397
46 T 1.000** 3.398
63 Q 0.888 3.119
75 Q 0.685 2.612
78 Y 0.813 2.937
107 E 0.998** 3.394
110 C 0.970* 3.324
126 T 1.000** 3.399
128 E 0.978* 3.345
156 K 0.807 2.918
176 P 0.848 3.020
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: S5_SFBB1)
Pr(w>1) post mean +- SE for w
8 L 0.648 2.455 +- 1.250
21 G 0.550 2.190 +- 1.271
36 R 0.878 3.129 +- 1.032
44 I 0.999** 3.484 +- 0.676
46 T 0.999** 3.485 +- 0.674
63 Q 0.858 3.086 +- 1.092
75 Q 0.622 2.402 +- 1.292
78 Y 0.745 2.738 +- 1.204
107 E 0.997** 3.478 +- 0.685
110 C 0.960* 3.373 +- 0.829
126 T 1.000** 3.486 +- 0.673
128 E 0.971* 3.407 +- 0.789
156 K 0.737 2.717 +- 1.218
176 P 0.799 2.906 +- 1.171
