--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Jul 11 18:00:18 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_5/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/DNG_N3/NS4A_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/NS4A_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -3640.23 -3687.98 2 -3644.73 -3696.54 -------------------------------------- TOTAL -3640.91 -3695.85 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/DNG_N3/NS4A_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/NS4A_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 8.660519 0.425873 7.415099 9.950002 8.637009 871.99 904.50 1.000 r(A<->C){all} 0.026296 0.000067 0.010330 0.041692 0.025610 734.99 750.99 1.000 r(A<->G){all} 0.230779 0.000636 0.183561 0.280790 0.229800 487.96 636.72 1.000 r(A<->T){all} 0.069101 0.000159 0.043629 0.092383 0.068821 767.20 849.14 1.002 r(C<->G){all} 0.020215 0.000064 0.006139 0.036322 0.019709 673.52 692.84 1.000 r(C<->T){all} 0.608553 0.000916 0.549104 0.665695 0.609714 467.70 550.97 1.000 r(G<->T){all} 0.045056 0.000152 0.022955 0.070210 0.043772 656.27 743.29 1.000 pi(A){all} 0.312290 0.000257 0.282375 0.345205 0.311999 665.82 799.20 1.001 pi(C){all} 0.256535 0.000219 0.228497 0.285311 0.256350 723.94 756.83 1.000 pi(G){all} 0.228667 0.000205 0.201849 0.258041 0.228500 960.38 997.21 1.000 pi(T){all} 0.202508 0.000155 0.178528 0.226854 0.202268 770.90 800.62 1.000 alpha{1,2} 0.235506 0.000519 0.193694 0.280474 0.233565 862.70 1035.32 1.000 alpha{3} 4.670807 1.007795 2.890384 6.680660 4.577061 1139.25 1285.10 1.000 pinvar{all} 0.050783 0.000731 0.001602 0.101547 0.047719 1044.84 1175.30 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 -2873.240253 Model 2: PositiveSelection -2872.958535 Model 0: one-ratio -2889.737012 Model 3: discrete -2851.251066 Model 7: beta -2857.294719 Model 8: beta&w>1 -2857.295396 Model 0 vs 1 32.99351800000022 Model 2 vs 1 0.5634359999994558 Model 8 vs 7 0.0013539999999920838
>C1 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C2 SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI PLQWIASAIVLEFFMMVLLIPEPEKQR >C3 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGKAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVIASSALLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C4 SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADI PLQWIASAIVLEFFMMVLLIPEPEKQR >C5 SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV PLQWIASAIVLEFFMMVLLIPEPEKQR >C6 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C7 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSALLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C8 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGKAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSALLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C9 oIALDLVTEIGRVPSoLoHRTRNoLDoLVMoHTSEoooRAYRHAVEEoPE TMETLoLoGLMIoLTGGAMLFLISoKGIGKTSIGLICVIVSSGMLWMoDo PLQWIAoAIVLEFFMMVoLIPEPEooR >C10 SMTLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGKAYQHALNELPE SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLIAIAVASGLLWVAEI QPQWIAASIILEFFLMVLLVPEPEKQR >C11 SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV PLQWIASAIVLEFFMMVLLIPEPEKQR >C12 SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMADV PLQWIASAIVLEFFMMVLLIPEPEKQR >C13 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C14 SVSGDLILEIGKLPQHLTLKAQNALDNLVMLHNSEQGGKAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C15 SIALDLVTEIGRVPTHLAHRTRNALDNLVMLHTSEHGGKAYRHAVEELPE TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI PLQWIASAIVLEFFMMVLLIPEPEKQR >C16 SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSALLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C17 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSVLLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C18 SITLDILTEIASLPTYLSSRAKLAPDNIVMLHTTERGGKAYQHALNELPE SLETLMLVALLGAMTAGIFLFFMQGKGMGKLSMGLIAIAVASGLLWVAEI QPQWIAASIILEFFLMALLIPEPEKQR >C19 SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV PLQWIASAIVLEFFMMVLLIPEPEKQR >C20 SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI QPHWIAASIILEFFLIVLLIPEPEKQR >C21 SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPE TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI QPHWIAASIILEFFLIVLLIPEPEKQR >C22 SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGKAYNHALSELPE TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI QPHWIAASIILEFFLIVLLIPEPEKQR >C23 SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI QPHWIAASIILEFFLIVLLIPEPEKQR >C24 SLTLSLITEMGRLPTFMTQKTRDALDNLAVLHSAEMGGRAYNHALSELPE TLETLLLLGLLATVTGGIFLFLMSGRGVGKMTLGMCCIITASGLLWYAQI QPHWIAASIILEFFLIVLLIPEPEKQR >C25 SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI QPHWIAASIILEFFLIVLLIPEPEKQR >C26 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSALLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C27 SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI PLQWIASAIVLEFFMMVLLIPEPEKQR >C28 SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI QPHWIAASIILEFFLIVLLIPEPEKQR >C29 SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPE TLETLLLLTLLATVTGGIFLFLMSGKGVGKMTLGMCCIITASILLWYAQI QPHWIAASIILEFFLIVLLIPEPEKQR >C30 SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI QPHWIAASIILEFFLIVLLIPEPEKQR >C31 SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAAI PLQWIASAIVLEFFMMVLLIPEPEKQR >C32 SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI QPHWIAASIILEFFLIVLLIPEPEKQR >C33 SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPE SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVAEI QPQWIAASIILEFFLMVLLIPEPEKQR >C34 SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIVTASILLWYAQI QPHWIAASIILEFFLIVLLIPEPEKQR >C35 SVSSDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGKAYRHAMEELPD TIETIMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVTSSSALLWMANV EPHWIAASIILEFFLMVLLIPEPDRQR >C36 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C37 SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGKAYNHALSELPE TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI QPHWIAASIILEFFLIVLLIPEPEKQR >C38 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLVLIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSVLLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C39 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C40 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSVLLWMGSV EPHWIAASIILEFFLMVLLIPEPDRQR >C41 SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEVGGRAYNHALSELPE TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI QPHWIAASIILEFFLIVLLIPEPEKQR >C42 SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMSWMAEI PLQWIASAIVLEFFMMVLLIPEPEKQR >C43 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSVLLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C44 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C45 SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPE SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVAEI QPQWIAASIILEFFLMVLLIPEPEKQR >C46 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C47 SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI PLQWIASAIVLEFFMMVLLIPEPEKQR >C48 SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSALLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR >C49 SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV PLQWIASAIVLEFFMMVLLIPEPEKQR >C50 SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVIASSVLLWMASV EPHWIAASIILEFFLMVLLIPEPDRQR 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 [0] 0 -out_lib W_F [0] no -out_lib_mode S [0] primary -lib_only D [0] 0 -outseqweight W_F [0] no -dpa FL [0] 0 -seq_source S [0] ANY -cosmetic_penalty D [0] 0 -gapopen D [0] 0 -gapext D [0] 0 -fgapopen D [0] 0 -fgapext D [0] 0 -nomatch D [0] 0 -newtree W_F [0] default -tree W_F [0] NO -usetree R_F [0] -tree_mode S [0] nj -distance_matrix_mode S [0] ktup -distance_matrix_sim_mode S [0] idmat_sim1 -quicktree FL [0] 0 -outfile W_F [0] default -maximise FL [1] 1 -output S [1] score_ascii html score_ascii -len D [0] 0 -infile R_F [1] input.prot.fasta.muscle_rs_0_0.fasta.aln -matrix S [0] default -tg_mode D [0] 1 -profile_mode S [0] cw_profile_profile -profile_comparison S [0] profile -dp_mode S [0] linked_pair_wise -ktuple D [0] 1 -ndiag D [0] 0 -diag_threshold D [0] 0 -diag_mode D [0] 0 -sim_matrix S [0] vasiliky -transform S [0] -extend_seq FL [0] 0 -outorder S [0] input -inorder S [0] aligned -seqnos S [0] off -case S [0] keep -cpu D [0] 0 -maxnseq D [0] 1000 -maxlen D [0] -1 -sample_dp D [0] 0 -weight S [0] default -seq_weight S [0] no -align FL [1] 1 -mocca FL [0] 0 -domain FL [0] 0 -start D [0] 0 -len D [0] 0 -scale D [0] 0 -mocca_interactive FL [0] 0 -method_evaluate_mode S [0] default -evaluate_mode S [1] t_coffee_fast -get_type FL [0] 0 -clean_aln D [0] 0 -clean_threshold D [1] 1 -clean_iteration D [1] 1 -clean_evaluate_mode S [0] t_coffee_fast -extend_matrix FL [0] 0 -prot_min_sim D [40] 40 -prot_max_sim D [90] 90 -prot_min_cov D [40] 40 -pdb_type S [0] d -pdb_min_sim D [35] 35 -pdb_max_sim D [100] 100 -pdb_min_cov D [50] 50 -pdb_blast_server W_F [0] EBI -blast W_F [0] -blast_server W_F [0] EBI -pdb_db W_F [0] pdb -protein_db W_F [0] uniprot -method_log W_F [0] no -struc_to_use S [0] -cache W_F [0] use -align_pdb_param_file W_F [0] no -align_pdb_hasch_mode W_F [0] hasch_ca_trace_bubble -external_aligner S [0] NO -msa_mode S [0] tree -master S [0] no -blast_nseq D [0] 0 -lalign_n_top D [0] 10 -iterate D [1] 0 -trim D [0] 0 -split D [0] 0 -trimfile S [0] default -split D [0] 0 -split_nseq_thres D [0] 0 -split_score_thres D [0] 0 -check_pdb_status D [0] 0 -clean_seq_name D [0] 0 -seq_to_keep S [0] -dpa_master_aln S [0] -dpa_maxnseq D [0] 0 -dpa_min_score1 D [0] -dpa_min_score2 D [0] -dpa_keep_tmpfile FL [0] 0 -dpa_debug D [0] 0 -multi_core S [0] templates_jobs_relax_msa_evaluate -n_core D [0] 0 -max_n_proc D [0] 0 -lib_list S [0] -prune_lib_mode S [0] 5 -tip S [0] none -rna_lib S [0] -no_warning D [0] 0 -run_local_script D [0] 0 -plugins S [0] default -proxy S [0] unset -email S [0] -clean_overaln D [0] 0 -overaln_param S [0] -overaln_mode S [0] -overaln_model S [0] -overaln_threshold D [0] 0 -overaln_target D [0] 0 -overaln_P1 D [0] 0 -overaln_P2 D [0] 0 -overaln_P3 D [0] 0 -overaln_P4 D [0] 0 -exon_boundaries S [0] -dump S [0] no -display D [0] 100 INPUT FILES Input File (S) input.