--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sun Feb 11 13:36:11 WET 2018
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=/usr/bin/
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb
tcoffee.bin=t_coffee
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/HIV1_N2/POL_1_3/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_3/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/HIV1_N2/POL_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -32411.62 -32455.16
2 -32412.44 -32451.69
--------------------------------------
TOTAL -32411.95 -32454.50
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_3/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/HIV1_N2/POL_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 4.412408 0.021471 4.145539 4.711587 4.409860 663.62 705.10 1.000
r(A<->C){all} 0.073778 0.000014 0.066835 0.080844 0.073671 646.73 682.76 1.000
r(A<->G){all} 0.346123 0.000178 0.319883 0.371248 0.346186 356.69 404.03 1.002
r(A<->T){all} 0.034767 0.000007 0.030161 0.040460 0.034644 689.19 692.07 1.000
r(C<->G){all} 0.040412 0.000016 0.032595 0.048187 0.040191 646.37 720.41 1.000
r(C<->T){all} 0.462400 0.000205 0.435443 0.491306 0.462243 352.86 393.69 1.002
r(G<->T){all} 0.042520 0.000013 0.035538 0.049704 0.042426 749.95 836.96 1.000
pi(A){all} 0.417173 0.000051 0.402278 0.430204 0.417234 429.63 474.45 1.000
pi(C){all} 0.175578 0.000027 0.164797 0.184846 0.175477 462.58 552.23 1.001
pi(G){all} 0.203208 0.000033 0.193026 0.215333 0.203088 496.46 612.03 1.000
pi(T){all} 0.204042 0.000032 0.193506 0.215355 0.204010 680.97 682.94 1.000
alpha{1,2} 0.298749 0.000226 0.268436 0.327047 0.298491 941.75 1131.59 1.000
alpha{3} 2.193268 0.043366 1.819823 2.619593 2.185551 1180.09 1224.23 1.000
pinvar{all} 0.238728 0.000304 0.203745 0.271047 0.238809 900.61 956.17 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 -31434.778169
Model 2: PositiveSelection -31345.916802
Model 0: one-ratio -33050.813068
Model 3: discrete -31176.003452
Model 7: beta -31228.681779
Model 8: beta&w>1 -31116.540357
Model 0 vs 1 3232.069798000004
Model 2 vs 1 177.72273400000267
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: B.BR.10.10BR_PE019.KT427740_)
Pr(w>1) post mean +- SE for w
17 S 0.990* 3.165
32 A 0.905 2.979
36 L 0.999** 3.186
37 N 0.559 2.222
101 P 1.000** 3.188
260 E 0.962* 3.103
348 Q 0.961* 3.102
382 K 1.000** 3.188
423 T 0.673 2.472
471 Q 1.000** 3.187
513 S 0.891 2.949
589 L 0.938 3.052
605 P 0.997** 3.181
620 H 0.988* 3.161
691 S 1.000** 3.188
798 I 0.938 3.051
816 S 0.958* 3.097
821 N 1.000** 3.188
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.BR.10.10BR_PE019.KT427740_)
Pr(w>1) post mean +- SE for w
17 S 0.994** 3.271 +- 0.445
32 A 0.940 3.141 +- 0.675
35 S 0.534 2.192 +- 1.160
36 L 0.999** 3.282 +- 0.415
37 N 0.638 2.403 +- 1.119
101 P 1.000** 3.283 +- 0.412
131 L 0.515 2.131 +- 1.146
260 E 0.975* 3.224 +- 0.541
348 Q 0.976* 3.227 +- 0.537
382 K 1.000** 3.283 +- 0.412
423 T 0.766 2.722 +- 1.025
471 Q 1.000** 3.283 +- 0.413
513 S 0.935 3.132 +- 0.690
589 L 0.963* 3.197 +- 0.591
605 P 0.998** 3.280 +- 0.422
620 H 0.993** 3.267 +- 0.453
628 L 0.529 2.140 +- 1.130
691 S 1.000** 3.283 +- 0.412
798 I 0.966* 3.204 +- 0.581
816 S 0.972* 3.217 +- 0.553
821 N 1.000** 3.283 +- 0.412
Model 8 vs 7 224.28284399999393
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.BR.10.10BR_PE019.KT427740_)
Pr(w>1) post mean +- SE for w
5 T 0.636 1.567
17 S 1.000** 2.088
18 S 0.530 1.413
21 T 0.936 1.996
28 R 0.759 1.743
30 D 0.966* 2.039
32 A 0.998** 2.086
35 S 0.911 1.960
36 L 1.000** 2.089
37 N 0.994** 2.080
38 L 0.572 1.470
99 Q 0.501 1.368
101 P 1.000** 2.089
131 L 0.948 2.014
260 E 1.000** 2.088
348 Q 1.000** 2.088
382 K 1.000** 2.089
423 T 0.992** 2.077
471 Q 1.000** 2.089
483 F 0.888 1.928
494 M 0.987* 2.070
513 S 0.996** 2.083
514 T 0.731 1.702
523 I 0.915 1.967
572 A 0.699 1.657
589 L 0.999** 2.087
605 P 1.000** 2.088
620 H 1.000** 2.088
628 L 0.990* 2.074
691 S 1.000** 2.089
769 I 0.646 1.580
798 I 0.998** 2.086
816 S 1.000** 2.088
821 N 1.000** 2.089
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.BR.10.10BR_PE019.KT427740_)
Pr(w>1) post mean +- SE for w
17 S 0.998** 2.496 +- 0.075
21 T 0.786 2.154 +- 0.666
30 D 0.618 1.892 +- 0.776
32 A 0.984* 2.475 +- 0.197
35 S 0.821 2.207 +- 0.629
36 L 1.000** 2.500 +- 0.027
37 N 0.917 2.368 +- 0.440
101 P 1.000** 2.500 +- 0.001
131 L 0.813 2.199 +- 0.631
260 E 0.993** 2.489 +- 0.129
348 Q 0.993** 2.489 +- 0.131
382 K 1.000** 2.500 +- 0.001
423 T 0.947 2.415 +- 0.359
471 Q 1.000** 2.500 +- 0.013
483 F 0.582 1.825 +- 0.800
494 M 0.558 1.801 +- 0.787
513 S 0.982* 2.471 +- 0.215
523 I 0.549 1.775 +- 0.803
589 L 0.986* 2.477 +- 0.188
605 P 0.999** 2.499 +- 0.047
620 H 0.997** 2.495 +- 0.087
628 L 0.883 2.313 +- 0.513
691 S 1.000** 2.500 +- 0.001
798 I 0.986* 2.478 +- 0.184
816 S 0.993** 2.489 +- 0.131
821 N 1.000** 2.500 +- 0.003
