--- 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) -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]