--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Jul 11 03:09:26 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_3/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_N3/NS4A_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/NS4A_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_N3/NS4A_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -3649.06 -3698.58
2 -3649.37 -3696.21
--------------------------------------
TOTAL -3649.20 -3697.98
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_N3/NS4A_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/NS4A_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_N3/NS4A_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} 8.635339 0.433553 7.462612 10.081880 8.625848 918.75 950.66 1.000
r(A<->C){all} 0.029162 0.000076 0.012416 0.045706 0.028648 710.10 772.91 1.000
r(A<->G){all} 0.223048 0.000623 0.175226 0.272317 0.222653 460.76 572.48 1.000
r(A<->T){all} 0.070170 0.000159 0.048357 0.097240 0.069425 694.35 806.58 1.000
r(C<->G){all} 0.015883 0.000069 0.000799 0.031497 0.014855 562.43 722.35 1.001
r(C<->T){all} 0.619607 0.000918 0.554356 0.674514 0.620210 566.99 631.40 1.001
r(G<->T){all} 0.042131 0.000146 0.019135 0.064986 0.041420 774.37 829.94 1.003
pi(A){all} 0.309824 0.000259 0.276517 0.339625 0.309986 841.92 864.57 1.001
pi(C){all} 0.247676 0.000222 0.217510 0.275068 0.247809 772.97 798.19 1.001
pi(G){all} 0.236724 0.000210 0.209267 0.265741 0.236594 649.58 702.87 1.000
pi(T){all} 0.205775 0.000167 0.181126 0.231578 0.205291 776.31 833.94 1.000
alpha{1,2} 0.231096 0.000473 0.187919 0.273066 0.229925 1340.49 1420.75 1.000
alpha{3} 4.404865 0.973416 2.613763 6.329489 4.291220 1159.58 1330.29 1.000
pinvar{all} 0.039734 0.000653 0.000042 0.087045 0.035043 1072.15 1161.00 1.001
------------------------------------------------------------------------------------------------------
* 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 -3340.425291
Model 2: PositiveSelection -3340.425291
Model 0: one-ratio -3356.040895
Model 3: discrete -3314.907039
Model 7: beta -3317.744351
Model 8: beta&w>1 -3317.619339
Model 0 vs 1 31.23120800000015
Model 2 vs 1 0.0
Model 8 vs 7 0.2500239999999394
>C1
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLIPEPEKQR
>C2
SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C3
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C4
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C5
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGoGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C6
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGKAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C7
SVSGDLILEIGKLPQHLTQKAQKALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C8
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C9
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLIPEPEKQR
>C10
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLFWVAEI
QPQWIAASIILEFFLMVLLIPEPEKQR
>C11
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEVGGKAYTHALSELPE
TLETLLLLTLLAAVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C12
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C13
SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C14
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGVGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C15
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLIPEPEKQR
>C16
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSALLWMANV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C17
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEVGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGVGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C18
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C19
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C20
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C21
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C22
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEVGGKAYTHALSELPE
TLETLLLLTLLAAVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C23
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C24
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C25
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C26
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGVGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C27
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGKAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLIAIAVASGoLWVAEI
QPQWIAASIILEFFLMVLLVPEPEKQR
>C28
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGVGKTSIGLICVVASSGMLWMADI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C29
SLTLSLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C30
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASVLLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C31
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASVLLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C32
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C33
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMSWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C34
SITLDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C35
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEVGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGVGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C36
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMSSSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C37
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C38
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C39
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C40
SLTLNIITEMGRLPTFMTQKTRDALDNLAVLHSAEMGGRAYNHALSELPE
TLETLLLLGLLATVTGGIFLFLMSGRGVGKMTLGMCCIITASGLLWYAQI
QPHWIAASIILEFFLTVLLIPEPEKQR
>C41
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C42
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C43
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGKAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLIAIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLVPEPEKQR
>C44
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASVLLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C45
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C46
SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHoAEMGGRAYNHALSELPE
TLETLLLLGLLATVTGGIFLFLMSGRGVGKMTLGMCCIITASGLLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C47
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYKHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C48
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C49
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C50
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR
PROGRAM: T-COFFEE Version_10.00.r1613 (2013-10-22 15:49:04 - Revision 1613 - Build 427)
-full_log S [0]
-genepred_score S [0] nsd
-run_name S [0]
-mem_mode S [0] mem
-extend D [1] 1
-extend_mode S [0] very_fast_triplet
-max_n_pair D [0] 10
-seq_name_for_quadruplet S [0] all
-compact S [0] default
-clean S [0] no
-do_self FL [0] 0
-do_normalise D [0] 1000
-template_file S [0]
-setenv S [0] 0
-template_mode S [0]
-flip D [0] 0
-remove_template_file D [0] 0
-profile_template_file S [0]
-in S [0]
-seq S [0]
-aln S [0]
-method_limits S [0]
-method S [0]
-lib S [0]
-profile S [0]
-profile1 S [0]
-profile2 S [0]
-pdb S [0]
-relax_lib D [0] 1
-filter_lib D [0] 0
-shrink_lib D
