--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Tue Jul 10 15:24:55 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_N3/NS4A_1/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_N3/NS4A_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/NS4A_1/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_N3/NS4A_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -3528.18 -3574.71
2 -3532.38 -3580.06
--------------------------------------
TOTAL -3528.86 -3579.37
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_N3/NS4A_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/NS4A_1/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_N3/NS4A_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 8.456675 0.426215 7.093962 9.668426 8.432183 761.79 791.38 1.000
r(A<->C){all} 0.036139 0.000089 0.017704 0.054010 0.035601 610.14 686.79 1.001
r(A<->G){all} 0.183513 0.000469 0.141622 0.226421 0.182617 556.24 556.64 1.000
r(A<->T){all} 0.063157 0.000164 0.038281 0.087598 0.062719 480.00 705.61 1.001
r(C<->G){all} 0.022648 0.000069 0.006951 0.038888 0.021898 748.31 784.75 1.001
r(C<->T){all} 0.663994 0.000803 0.608890 0.717170 0.664357 467.37 471.95 1.000
r(G<->T){all} 0.030549 0.000112 0.011404 0.051316 0.029666 601.59 698.32 1.001
pi(A){all} 0.315423 0.000256 0.285827 0.347238 0.315308 802.92 811.71 1.000
pi(C){all} 0.241324 0.000205 0.215441 0.269950 0.241241 907.08 984.58 1.000
pi(G){all} 0.238996 0.000224 0.209621 0.267523 0.238920 907.72 909.37 1.000
pi(T){all} 0.204257 0.000164 0.181733 0.231955 0.203776 584.00 690.71 1.001
alpha{1,2} 0.216387 0.000372 0.180353 0.252996 0.214941 1144.82 1250.65 1.000
alpha{3} 3.890149 0.808324 2.267273 5.698821 3.770640 1208.96 1310.38 1.000
pinvar{all} 0.036937 0.000663 0.000010 0.085391 0.032124 1076.25 1192.18 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 -2964.097505
Model 2: PositiveSelection -2964.097505
Model 0: one-ratio -2964.520376
Model 3: discrete -2930.512289
Model 7: beta -2933.669647
Model 8: beta&w>1 -2933.670766
Model 0 vs 1 0.8457419999995182
Model 2 vs 1 0.0
Model 8 vs 7 0.002238000000033935
>C1
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPE
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C2
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGKAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLIAIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLVPEPEKQR
>C3
SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C4
SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C5
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C6
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C7
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C8
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C9
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C10
SIALDLVTEIGRVPTHLAHRTRNALDNLVMLHTSEHGGKAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C11
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C12
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C13
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASVLLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C14
SIALDLVTEIGRVPSHLAHRTRNALDNLVMoHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEoQR
>C15
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVVASSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C16
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C17
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEVGGKAYTHALSELPE
TLETLLLLTLLAAVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C18
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGKAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGMGKLSMGLIAIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLVPEPEKQR
>C19
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C20
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C21
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETIMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVTSSSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C22
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGVGKMTLGMCCIITASILLWHAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C23
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C24
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGVGKTSIGLICVVASSGMLWMADI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C25
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGVGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C26
SVSGDLILEIGKLPQHLTQKAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C27
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVMLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C28
SLTMNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C29
SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C30
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKoR
>C31
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVMLFFLSGKGLGKTSIGLLCVMASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C32
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C33
SIALDLVTEIGRVPTHLAHRTRNALDNLVMLHTSEHGGKAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C34
SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C35
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKRSIGLLCVTASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C36
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C37
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C38
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C39
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEVGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C40
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C41
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C42
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEVGGKAHTHALSELPE
TLETLLLLTLLAAVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C43
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLAAVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C44
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLIPEPEKQR
>C45
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C46
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C47
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C48
SLTLNLITEMGRLPTLMTQKARDALDNLAVLHTAEVGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C49
SIALDLVTEIGRVPSHoAHRTRNoLDNLVMLHTSEHGGRAYRHoVEELPE
TMEoLLLLGLMILoTGGAMLFLISGKGIGKTSIGLICVIASSGMoWMAoo
PoQWIASAIVLoFoMMVLoIPEPEoQR
>C50
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
PROGRAM: T-COFFEE Version_10.00.r1613 (2013-10-22 15:49:04 - Revision 1613 - Build 427)
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-dump S [0] no
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