--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sat Jun 16 02:03:04 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_A2/prM_4/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/DNG_A2/prM_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A2/prM_4/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_A2/prM_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -4861.89 -4905.98 2 -4861.42 -4908.04 -------------------------------------- TOTAL -4861.63 -4907.47 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/DNG_A2/prM_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A2/prM_4/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_A2/prM_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 6.739662 0.246956 5.788081 7.670063 6.715648 781.56 804.04 1.000 r(A<->C){all} 0.052217 0.000077 0.034991 0.069143 0.051885 812.98 888.11 1.000 r(A<->G){all} 0.220210 0.000527 0.180503 0.269653 0.218739 494.49 577.64 1.000 r(A<->T){all} 0.063588 0.000100 0.045759 0.084553 0.063026 838.76 871.51 1.000 r(C<->G){all} 0.033207 0.000058 0.019261 0.048486 0.032627 880.68 931.99 1.000 r(C<->T){all} 0.597033 0.000821 0.538975 0.652127 0.597894 489.44 513.03 1.000 r(G<->T){all} 0.033745 0.000073 0.017497 0.050384 0.033273 839.81 847.86 1.000 pi(A){all} 0.304078 0.000212 0.277432 0.333730 0.304087 724.16 877.42 1.000 pi(C){all} 0.248129 0.000167 0.225317 0.273644 0.247831 745.76 809.54 1.001 pi(G){all} 0.248157 0.000204 0.220457 0.275890 0.247833 820.09 829.47 1.000 pi(T){all} 0.199637 0.000132 0.177762 0.221557 0.199538 835.99 847.56 1.000 alpha{1,2} 0.239808 0.000431 0.201893 0.280692 0.237961 1196.27 1256.49 1.000 alpha{3} 4.143853 0.770224 2.646392 5.957481 4.054756 1388.92 1444.96 1.000 pinvar{all} 0.058666 0.000744 0.006122 0.107719 0.057620 1294.23 1339.34 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 -4609.876674 Model 2: PositiveSelection -4609.876674 Model 0: one-ratio -4630.288405 Model 3: discrete -4559.303626 Model 7: beta -4564.313749 Model 8: beta&w>1 -4564.314728 Model 0 vs 1 40.82346200000029 Model 2 vs 1 0.0 Model 8 vs 7 0.001958000000740867
>C1 FHLTSRDGEPRMIVGKNERGKSLLFKTASGTNMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C2 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVMALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C3 FHLTTRNGEPHMIVSRQEKGKSLLFKTGDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C4 FHLTSRDGEPRMIVGKSERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C5 FHLTTRNGEPHMIVSRQEKGKSLLFKTENGVNMCTLMAMDLGELCEDTIT YNCPLLKQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWVLRHPGFTVMAAILAYTIGTTYFQ RVLIFILLTAVAPSMT >C6 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITGAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIAFFLAHAIGTSITQ KGIIFILLMLVTPSMA >C7 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITETEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C8 FHLTTRNGEPHMIVSKHEKGKSLLFKTEDGMNMCTLMAMDLGELCEDTIT YKCPFLKQNEPEDIDCWCNATSTWVTYGTCSTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKQAQRIETWILRHPGFTLMAAILAYTIGTTHFQ KILIFVLLTAVAPSMT >C9 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRNKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMA >C10 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWAFRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMA >C11 FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTMGEHRRQKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTMMAAILAYTIGTTHFQ RALIFILLTAVTPSMT >C12 FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ RVLIFTLLTAVAPSMT >C13 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIADVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C14 FHLTTRGGEPHMIVSKQERGKSLLFKTSGGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C15 FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTAPGDHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTYFQ RVLILILLTAVAPSMT >C16 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYTGTSLTQ KVVIFILLMLVTPSMT >C17 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFTLLMLVTPSMT >C18 FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCYQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C19 FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTVT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAHTIGTTYFQ RVLIFILLTAVAPSMT >C20 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNVTDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C21 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTTMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C22 FHLTTRGGEPHMIVSKHERGKALLFKTSTGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C23 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPQITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C24 FHLTSRDGEPRMIVAKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWVLRHPGFTILALFLAHYIGTSLTQ KVVVFTLLMLVTPSMT >C25 FHLTTRGGEPHMVVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTLT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C26 FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSRTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C27 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITETEPDDVDCWCNATETWVTYGTCSQAGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSoo >C28 FPISTSNGEPHMIVSRQEKGKSVNLKTEDGVNTYTLMAMDINEVCEDTIT YRRTTEGKKEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTYFQ RVLIFILLTAVAPSMT >C29 FHLTTRGGEQPMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHQREKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIAFFLAHAIGTSITQ KGIIFILLMLVTPSMA >C30 FHLTTRNGEPHMIVSRQEKGKSLLFKTKDGTNMCTLMAMDLGELCEDTIT YKCPFLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIEIWILRHPGFTIMAAILAYTIGTTHFQ RVLIFILLTAIAPSMT >C31 FHLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVT YKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKRSVALTPHSG MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ RTVFFVLMMLVAPSYG >C32 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPQITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIAFFLAHAIGTSITQ KGIIFILLMLVTPSMA >C33 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGEFCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLVLVTPSMA >C34 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C35 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCDDTMT YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C36 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILANTIGTTHFQ RALIFILLTAVAPSMT >C37 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C38 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYISTSLTQ KVVIFILLMLVTPSMT >C39 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGDMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMA >C40 FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDRRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C41 FHLTSRDGEPRMIVGKNERGKSLLFKTATGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSAWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLIQ KVVIFILLMLVTPSMT >C42 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C43 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVTALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C44 FHLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVT YKCPLLVNTEPEDIDCWCNLTSAWVMYGTCTQSGERRREKRSVALTPHSG MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ RTVFFILMMLVAPSYG >C45 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTLT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C46 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGINMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C47 FHLSTRDGEPLMIVAKHERGRPLLFKTTEGTNKCTLIAMDLGEMCEDTVT YKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKRSVALTPHSG MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ RTVFFVLMMLVAPSYG >C48 FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C49 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHIQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C50 FHLTSRDGEPRMIVGKNERGKSLLFKTASGIIKCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGERRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT 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.prot.fasta.muscle_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 50 SEQUENCES [PROTEIN] Multi Core Mode: 72 processors: -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.prot.fasta.muscle_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 50 SEQUENCES [PROTEIN] Multi Core Mode: 72 processors: --- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln -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.prot.fasta.muscle_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 50 SEQUENCES [PROTEIN] Multi Core Mode: 72 processors: --- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln -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.prot.fasta.muscle_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 50 SEQUENCES [PROTEIN] Multi Core Mode: 72 processors: --- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln -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.prot.fasta.muscle_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 50 SEQUENCES [PROTEIN] Multi Core Mode: 72 processors: --- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln -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.prot.fasta.muscle_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 50 SEQUENCES [PROTEIN] Multi Core Mode: 72 processors: --- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln -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.prot.fasta.muscle_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 50 SEQUENCES [PROTEIN] Multi Core Mode: 72 processors: --- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln -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.prot.fasta.muscle_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 50 SEQUENCES [PROTEIN] Multi Core Mode: 72 processors: --- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln -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.prot.fasta.muscle_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 50 SEQUENCES [PROTEIN] Multi Core Mode: 72 processors: --- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln -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.prot.fasta.muscle_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 50 SEQUENCES [PROTEIN] Multi Core Mode: 72 processors: --- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln -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.prot.fasta.muscle_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 50 SEQUENCES [PROTEIN] Multi Core Mode: 72 processors: --- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln -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.prot.fasta.muscle_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 50 SEQUENCES [PROTEIN] Multi Core Mode: 72 processors: --- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln -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.prot.fasta.muscle_rs_0_0.fasta.aln Format clustal_aln Input File (M) proba_pair Identify Master Sequences [no]: Master Sequences Identified INPUT SEQUENCES: 50 SEQUENCES [PROTEIN] Multi Core Mode: 72 processors: --- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln -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_bound