--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Mar 21 20:06:44 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=
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/ADOPS1/HIV1_AMINO/POL_1_2/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/HIV1_AMINO/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/POL_1_2/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/HIV1_AMINO/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -30942.29 -30982.07
2 -30942.63 -30983.10
--------------------------------------
TOTAL -30942.45 -30982.72
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/HIV1_AMINO/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/POL_1_2/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/HIV1_AMINO/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 3.652787 0.011993 3.452191 3.873230 3.650705 1115.91 1116.69 1.000
r(A<->C){all} 0.072830 0.000014 0.065885 0.080567 0.072817 613.00 704.96 1.000
r(A<->G){all} 0.344438 0.000175 0.318355 0.369014 0.344282 420.44 458.08 1.005
r(A<->T){all} 0.036124 0.000007 0.031290 0.041551 0.036063 639.98 671.52 1.000
r(C<->G){all} 0.041966 0.000017 0.033663 0.049850 0.041881 513.94 548.55 1.000
r(C<->T){all} 0.460174 0.000201 0.432905 0.486998 0.460490 390.13 432.02 1.003
r(G<->T){all} 0.044467 0.000014 0.037350 0.052013 0.044417 703.42 767.98 1.000
pi(A){all} 0.409925 0.000050 0.395978 0.423599 0.410037 599.69 630.68 1.000
pi(C){all} 0.175991 0.000031 0.165953 0.187764 0.175924 544.01 599.83 1.002
pi(G){all} 0.207995 0.000033 0.197249 0.219535 0.207807 486.44 505.96 1.001
pi(T){all} 0.206089 0.000034 0.195426 0.218109 0.206094 511.83 551.81 1.000
alpha{1,2} 0.290473 0.000219 0.264507 0.321968 0.289507 1052.83 1088.38 1.000
alpha{3} 2.508548 0.061651 2.049025 3.007293 2.495418 1238.74 1241.53 1.000
pinvar{all} 0.276282 0.000290 0.243388 0.309045 0.276442 1100.84 1105.65 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 -29918.976986
Model 2: PositiveSelection -29837.573841
Model 0: one-ratio -31500.878468
Model 3: discrete -29708.908189
Model 7: beta -29760.429703
Model 8: beta&w>1 -29659.144059
Model 0 vs 1 3163.802963999995
Model 2 vs 1 162.80629000000044
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.US.89.P896_89_6.U39362_)
Pr(w>1) post mean +- SE for w
17 S 0.836 2.826
34 N 0.964* 3.105
36 L 0.997** 3.177
101 D 1.000** 3.183
260 D 0.983* 3.146
344 Q 0.602 2.314
348 K 0.999** 3.180
382 V 1.000** 3.183
423 T 0.992** 3.165
471 Q 0.748 2.633
513 A 0.988* 3.157
589 S 0.968* 3.112
605 S 0.991** 3.162
620 H 0.988* 3.157
691 A 1.000** 3.183
821 T 1.000** 3.183
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.US.89.P896_89_6.U39362_)
Pr(w>1) post mean +- SE for w
17 S 0.896 3.049 +- 0.798
34 N 0.975* 3.236 +- 0.536
36 L 0.998** 3.292 +- 0.413
101 D 1.000** 3.295 +- 0.403
260 D 0.989* 3.270 +- 0.467
344 Q 0.701 2.574 +- 1.090
348 K 0.999** 3.294 +- 0.408
382 V 1.000** 3.295 +- 0.404
423 T 0.995** 3.285 +- 0.431
471 Q 0.812 2.839 +- 0.965
513 A 0.993** 3.281 +- 0.442
589 S 0.979* 3.246 +- 0.516
605 S 0.995** 3.285 +- 0.433
620 H 0.993** 3.279 +- 0.445
691 A 1.000** 3.295 +- 0.403
821 T 1.000** 3.295 +- 0.403
Model 8 vs 7 202.57128800000646
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.US.89.P896_89_6.U39362_)
Pr(w>1) post mean +- SE for w
12 K 0.862 2.147
17 S 0.985* 2.350
21 T 0.667 1.824
34 N 0.999** 2.372
36 L 1.000** 2.373
37 S 0.833 2.099
38 F 0.760 1.978
101 D 1.000** 2.374
260 D 1.000** 2.373
299 S 0.965* 2.315
344 Q 0.970* 2.325
348 K 1.000** 2.374
382 V 1.000** 2.374
423 T 1.000** 2.373
471 Q 0.985* 2.349
513 A 0.999** 2.372
572 V 0.766 1.988
589 S 0.999** 2.372
605 S 0.999** 2.372
620 H 0.999** 2.373
691 A 1.000** 2.374
821 T 1.000** 2.374
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.US.89.P896_89_6.U39362_)
Pr(w>1) post mean +- SE for w
12 K 0.784 2.155 +- 0.659
17 S 0.979* 2.467 +- 0.227
21 T 0.679 1.977 +- 0.763
34 N 0.996** 2.494 +- 0.100
36 L 1.000** 2.499 +- 0.035
37 S 0.757 2.110 +- 0.688
38 F 0.782 2.145 +- 0.675
101 D 1.000** 2.500 +- 0.004
260 D 0.998** 2.497 +- 0.071
299 S 0.924 2.379 +- 0.421
344 Q 0.939 2.403 +- 0.380
348 K 1.000** 2.500 +- 0.025
382 V 1.000** 2.500 +- 0.008
423 T 0.999** 2.498 +- 0.056
471 Q 0.967* 2.448 +- 0.283
513 A 0.998** 2.497 +- 0.067
572 V 0.511 1.724 +- 0.795
589 S 0.996** 2.494 +- 0.100
605 S 0.998** 2.497 +- 0.065
620 H 0.998** 2.497 +- 0.066
691 A 1.000** 2.500 +- 0.004
821 T 1.000** 2.500 +- 0.006
