--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu May 10 16:41:59 WEST 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/DNG_N2/NS2B_3/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_N2/NS2B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N2/NS2B_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/ADOPS1/DNG_N2/NS2B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -3539.22 -3590.13
2 -3543.61 -3585.44
--------------------------------------
TOTAL -3539.90 -3589.44
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_N2/NS2B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N2/NS2B_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/ADOPS1/DNG_N2/NS2B_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} 7.522369 0.330064 6.445980 8.689019 7.503303 1069.88 1102.57 1.000
r(A<->C){all} 0.059563 0.000169 0.035817 0.085609 0.058660 751.82 813.96 1.001
r(A<->G){all} 0.256235 0.000712 0.200860 0.305538 0.256005 478.48 554.40 1.000
r(A<->T){all} 0.088500 0.000197 0.059575 0.114151 0.087793 862.16 987.45 1.000
r(C<->G){all} 0.064357 0.000186 0.040182 0.093395 0.063934 656.21 755.86 1.000
r(C<->T){all} 0.522927 0.001035 0.464147 0.588314 0.522538 474.07 571.10 1.000
r(G<->T){all} 0.008418 0.000043 0.000006 0.021095 0.007029 881.07 915.15 1.002
pi(A){all} 0.325580 0.000247 0.295965 0.356686 0.325172 1062.48 1107.07 1.000
pi(C){all} 0.216695 0.000189 0.189690 0.243669 0.216382 858.19 968.75 1.000
pi(G){all} 0.237463 0.000212 0.209627 0.265927 0.237399 691.55 789.41 1.000
pi(T){all} 0.220262 0.000191 0.192226 0.246337 0.220087 697.15 816.62 1.000
alpha{1,2} 0.224549 0.000667 0.174714 0.274691 0.222906 1287.87 1333.52 1.000
alpha{3} 3.996541 0.884805 2.303337 5.823713 3.898486 1476.21 1488.61 1.000
pinvar{all} 0.051378 0.000565 0.008576 0.098992 0.049857 1380.00 1440.50 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 -3176.572722
Model 2: PositiveSelection -3176.572722
Model 0: one-ratio -3179.853132
Model 3: discrete -3158.121053
Model 7: beta -3159.055428
Model 8: beta&w>1 -3159.052072
Model 0 vs 1 6.560820000000604
Model 2 vs 1 0.0
Model 8 vs 7 0.006712000000334228
>C1
SWPLNEGIMAVGLVSLLGSALLKNDVPLAGPMVAGGLLLAAYVMSGSSAD
LSLEKAANVQWDEMADITGSSPIIEVKQDEDGSFSIRDVEETNMITLLVK
LALITVSGLYPLAIPVTMALWYIWQVKTQR
>C2
SWPLNEGVMAVGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD
LTVEKAADITWEEEAEQTGVSHNLMITVDDDGTMRIKDDETENILTVLLK
TALLIVSGIFPYSIPATLLVWHTWQKQTQR
>C3
SWPLNEGIMAVGVVSILLSSLLKDDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPLSIPATLFVWYFWQKKKQR
>C4
SWPLNEGIMAVGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAVVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPLSIPATLFVWYFWQKKKQR
>C5
SWPLNEAIMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERAADVRWEEQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIR
TGLLVISGLFPVSIPITAAAWYLWEVKKQR
>C6
SWPLNEAVMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEHTLTILIR
TGLLVISGVFPVSIPITAAAWYLWEVKKQR
>C7
SWPLNEoVMAVoLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD
LTVEKAADVTWEEEAEQTGVSHNLMITVDDDGTMRIKDDETENILTVLLK
TALLIVSGIFPYSIPATLLVWHTWQKQTQR
>C8
SWPLNEGIMAIGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEDEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLVISGV
