--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Nov 12 05:59:25 WET 2016
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=/opt/ADOPS/2/Ac76E-PB/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/2/Ac76E-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/2/Ac76E-PB/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/ADOPS/2/Ac76E-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -12131.17 -12145.97
2 -12130.94 -12145.77
--------------------------------------
TOTAL -12131.05 -12145.88
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/2/Ac76E-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/2/Ac76E-PB/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/ADOPS/2/Ac76E-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 0.666378 0.001018 0.603050 0.728601 0.665846 1275.66 1358.12 1.000
r(A<->C){all} 0.132647 0.000146 0.109821 0.156891 0.132582 1005.01 1050.32 1.001
r(A<->G){all} 0.278340 0.000339 0.241040 0.313566 0.278260 946.94 972.63 1.000
r(A<->T){all} 0.085827 0.000159 0.060974 0.109506 0.085463 1037.27 1059.51 1.001
r(C<->G){all} 0.079050 0.000063 0.064226 0.094478 0.078811 1127.22 1142.31 1.000
r(C<->T){all} 0.355959 0.000409 0.313515 0.392686 0.355905 874.12 988.88 1.000
r(G<->T){all} 0.068177 0.000081 0.051651 0.086160 0.067893 1076.63 1195.60 1.000
pi(A){all} 0.223849 0.000039 0.212664 0.237145 0.223819 1052.84 1077.46 1.000
pi(C){all} 0.295655 0.000047 0.282394 0.309138 0.295773 1126.27 1185.43 1.000
pi(G){all} 0.271482 0.000042 0.258031 0.283527 0.271389 1135.13 1180.08 1.000
pi(T){all} 0.209015 0.000035 0.197936 0.221179 0.209031 1118.49 1148.05 1.000
alpha{1,2} 0.157826 0.000187 0.131535 0.183751 0.157381 1172.32 1330.47 1.000
alpha{3} 4.373407 1.022544 2.531397 6.356688 4.259719 1333.12 1351.53 1.000
pinvar{all} 0.432578 0.000676 0.378363 0.480482 0.433712 1196.25 1285.13 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 -11272.307428
Model 2: PositiveSelection -11272.307428
Model 0: one-ratio -11473.124883
Model 3: discrete -11270.557945
Model 7: beta -11276.876824
Model 8: beta&w>1 -11272.854268
Model 0 vs 1 401.6349100000007
Model 2 vs 1 0.0
Model 8 vs 7 8.045112000003428
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Ac76E-PB)
Pr(w>1) post mean +- SE for w
29 T 0.861 1.903
517 I 0.870 1.918
520 T 0.959* 2.053
655 Q 0.641 1.566
923 K 0.731 1.705
931 E 0.980* 2.085
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: D_melanogaster_Ac76E-PB)
Pr(w>1) post mean +- SE for w
8 T 0.838 1.347 +- 0.359
16 N 0.820 1.330 +- 0.375
17 A 0.691 1.169 +- 0.514
19 A 0.574 1.027 +- 0.573
25 D 0.799 1.315 +- 0.379
29 T 0.963* 1.469 +- 0.159
202 T 0.584 1.041 +- 0.569
512 T 0.637 1.139 +- 0.496
515 T 0.755 1.265 +- 0.426
517 I 0.968* 1.474 +- 0.145
518 K 0.796 1.313 +- 0.380
520 T 0.984* 1.488 +- 0.096
541 P 0.581 1.037 +- 0.569
543 A 0.591 1.045 +- 0.570
544 I 0.525 1.014 +- 0.533
595 H 0.522 1.010 +- 0.535
602 N 0.864 1.378 +- 0.317
603 D 0.567 1.059 +- 0.525
605 E 0.900 1.413 +- 0.266
606 P 0.756 1.274 +- 0.411
655 Q 0.911 1.420 +- 0.264
672 G 0.664 1.137 +- 0.532
674 A 0.581 1.073 +- 0.523
923 K 0.946 1.456 +- 0.191
927 S 0.763 1.270 +- 0.426
928 T 0.711 1.223 +- 0.450
931 E 0.990* 1.493 +- 0.075
932 S 0.578 1.072 +- 0.521
934 F 0.518 0.969 +- 0.577
935 S 0.579 1.033 +- 0.572
938 V 0.825 1.333 +- 0.372
940 S 0.810 1.326 +- 0.370
947 L 0.556 1.021 +- 0.561
952 Y 0.859 1.368 +- 0.336
1005 M 0.754 1.272 +- 0.412
1008 D 0.891 1.404 +- 0.281
1009 A 0.758 1.265 +- 0.429
1012 T 0.793 1.301 +- 0.402
1013 H 0.546 0.995 +- 0.579
1271 T 0.663 1.163 +- 0.490
