--- 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