--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sun Jan 28 05:01:24 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_N1/GAG_1_3/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_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_N1/GAG_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -17439.59 -17491.80
2 -17441.55 -17483.87
--------------------------------------
TOTAL -17440.15 -17491.10
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_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_N1/GAG_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} 3.665210 0.017469 3.408917 3.924786 3.663371 1014.55 1113.01 1.000
r(A<->C){all} 0.085257 0.000028 0.074599 0.095353 0.085191 578.37 693.04 1.000
r(A<->G){all} 0.302350 0.000248 0.271668 0.333539 0.302333 174.99 217.26 1.001
r(A<->T){all} 0.043506 0.000016 0.036205 0.051691 0.043459 857.04 872.90 1.002
r(C<->G){all} 0.050841 0.000028 0.041122 0.061631 0.050633 840.14 843.58 1.000
r(C<->T){all} 0.451794 0.000330 0.414924 0.485958 0.451815 183.58 227.23 1.001
r(G<->T){all} 0.066252 0.000041 0.053859 0.078976 0.066211 616.08 649.30 1.005
pi(A){all} 0.413172 0.000089 0.394282 0.431264 0.413102 711.07 730.52 1.000
pi(C){all} 0.200829 0.000057 0.186678 0.216176 0.200821 504.44 578.66 1.000
pi(G){all} 0.208460 0.000063 0.192474 0.223696 0.208426 554.04 623.38 1.000
pi(T){all} 0.177539 0.000058 0.162696 0.192125 0.177546 446.82 521.37 1.000
alpha{1,2} 0.327520 0.000451 0.286598 0.368909 0.326647 1070.34 1132.39 1.000
alpha{3} 2.546008 0.106460 1.945496 3.213376 2.528353 1335.19 1338.71 1.000
pinvar{all} 0.199450 0.000453 0.159863 0.243377 0.199033 1075.99 1136.74 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 -15404.232647
Model 2: PositiveSelection -15340.797519
Model 0: one-ratio -16230.792918
Model 3: discrete -15268.416895
Model 7: beta -15312.704747
Model 8: beta&w>1 -15254.597723
Model 0 vs 1 1653.120541999997
Model 2 vs 1 126.87025600000197
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.CY.07.CY201.JF683753_)
Pr(w>1) post mean +- SE for w
77 Y 1.000** 3.067
82 V 1.000** 3.067
89 K 1.000** 3.067
91 E 0.972* 3.010
113 A 0.976* 3.017
134 P 1.000** 3.067
203 L 0.966* 2.996
211 I 0.684 2.414
240 N 0.997** 3.062
320 T 0.611 2.264
345 S 0.995** 3.058
360 N 1.000** 3.067
371 Q 0.931 2.924
447 Q 0.594 2.229
452 S 0.945 2.954
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.CY.07.CY201.JF683753_)
Pr(w>1) post mean +- SE for w
77 Y 1.000** 3.326 +- 0.379
82 V 1.000** 3.326 +- 0.380
89 K 1.000** 3.326 +- 0.379
91 E 0.957* 3.221 +- 0.602
113 A 0.968* 3.248 +- 0.556
134 P 1.000** 3.326 +- 0.379
203 L 0.959* 3.228 +- 0.593
211 I 0.588 2.329 +- 1.159
240 N 0.997** 3.319 +- 0.400
320 T 0.549 2.248 +- 1.172
345 S 0.995** 3.315 +- 0.411
360 N 1.000** 3.326 +- 0.380
371 Q 0.923 3.143 +- 0.721
447 Q 0.546 2.244 +- 1.176
452 S 0.934 3.168 +- 0.686
Model 8 vs 7 116.214047999998
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.CY.07.CY201.JF683753_)
Pr(w>1) post mean +- SE for w
77 Y 1.000** 2.453
82 V 1.000** 2.453
88 Q 0.515 1.695
89 K 1.000** 2.453
91 E 0.981* 2.423
113 A 0.983* 2.427
134 P 1.000** 2.453
203 L 0.976* 2.415
211 I 0.813 2.161
240 N 0.998** 2.449
320 T 0.767 2.087
345 S 0.997** 2.447
360 N 1.000** 2.452
371 Q 0.942 2.363
447 Q 0.720 2.011
452 S 0.968* 2.402
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.CY.07.CY201.JF683753_)
Pr(w>1) post mean +- SE for w
77 Y 1.000** 2.500 +- 0.005
82 V 1.000** 2.500 +- 0.013
88 Q 0.551 1.791 +- 0.787
89 K 1.000** 2.500 +- 0.006
91 E 0.982* 2.472 +- 0.208
113 A 0.985* 2.477 +- 0.188
134 P 1.000** 2.500 +- 0.006
203 L 0.979* 2.468 +- 0.223
211 I 0.842 2.251 +- 0.577
240 N 0.998** 2.496 +- 0.074
320 T 0.811 2.200 +- 0.624
345 S 0.997** 2.495 +- 0.086
360 N 1.000** 2.500 +- 0.023
371 Q 0.954* 2.427 +- 0.331
447 Q 0.775 2.140 +- 0.669
452 S 0.973* 2.458 +- 0.254
