--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Jun 15 18:32:45 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_3/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/DNG_A2/prM_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A2/prM_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_A2/prM_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -4165.53 -4211.56 2 -4166.14 -4215.63 -------------------------------------- TOTAL -4165.79 -4214.95 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/DNG_A2/prM_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A2/prM_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_A2/prM_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} 5.742301 0.201819 4.869434 6.653942 5.721698 758.64 818.32 1.000 r(A<->C){all} 0.041529 0.000080 0.025394 0.059846 0.041021 547.20 601.50 1.000 r(A<->G){all} 0.238438 0.000694 0.185056 0.287795 0.237011 459.99 511.54 1.000 r(A<->T){all} 0.065939 0.000122 0.044152 0.087205 0.065695 801.06 839.76 1.000 r(C<->G){all} 0.026804 0.000053 0.013541 0.041362 0.026183 763.74 842.33 1.000 r(C<->T){all} 0.594531 0.000981 0.534584 0.657250 0.596150 436.45 492.96 1.000 r(G<->T){all} 0.032759 0.000077 0.015907 0.050031 0.031907 872.85 901.57 1.002 pi(A){all} 0.291144 0.000225 0.260822 0.319138 0.291006 676.18 683.20 1.001 pi(C){all} 0.247681 0.000185 0.222041 0.274805 0.247641 731.41 798.71 1.000 pi(G){all} 0.244790 0.000220 0.215425 0.272958 0.244327 719.12 719.31 1.001 pi(T){all} 0.216385 0.000159 0.190977 0.240499 0.215979 673.00 719.93 1.000 alpha{1,2} 0.214912 0.000381 0.176266 0.253273 0.213274 1154.03 1209.85 1.000 alpha{3} 4.045538 0.812981 2.479430 5.866412 3.946351 1280.86 1388.32 1.000 pinvar{all} 0.081278 0.001171 0.011896 0.143467 0.080782 909.67 1155.05 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 -3982.45163 Model 2: PositiveSelection -3982.45163 Model 0: one-ratio -4025.939801 Model 3: discrete -3943.785617 Model 7: beta -3943.987698 Model 8: beta&w>1 -3943.987969 Model 0 vs 1 86.97634199999993 Model 2 vs 1 0.0 Model 8 vs 7 5.419999997684499E-4
>C1 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITETEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVTALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C2 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVMALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C3 FHLTSRDGEPRMIVAKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWVLRHPGFTILALFLAHYIGTSLTQ KVVVFTLLMLVTPSMT >C4 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALILILLTAVAPSMT >C5 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTLT YKCPRITEVEPDDVDCWCNTTDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRAETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C6 FHLTTRGGEPHMIVSKQERGKSLLFKTSVGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C7 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFMLLMLVTPSMT >C8 FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHVIGTSITQ KGIIFILLMLVTPSMA >C9 FHLTTRNGEPHMIVGIQEKGKSLLFKTENGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMA >C10 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPFIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFVLLMLVTPSMA >C11 FHLTIRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGEFCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C12 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRISEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C13 FHLTTRNGEPHMIVSRQEKGKSLLFKTKDGTNMCTLMAMDLGELCEDTIT YKCPFLKQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRRGKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ RVLIFILLTAIAPSMT >C14 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHTIGTSITQ KGIIFILLMLVTPSMA >C15 FHLTSRDGEPRMIVAKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFVLLMLVTPSMT >C16 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTIGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C17 FHLTTRNGEPHMIVSKHEKGKSLLFKTEDGMNMCTLMAMDLGELCEDTIT YKCPFLKQNEPEDIDCWCNATSTWVTYGTCSTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKQAQRIETWILRHPGFTLMAAILAYTIGTTHFQ KILIFILLTAVAPSMT >C18 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGINMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVTALFLAHAIGTSITQ KGIIFILLILVTPSMA >C19 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGEICEDTMT YKCPRITEAEPNHVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALALHEG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C20 FHLTTRNGEPHMIVSIQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C21 FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTVT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAHTIGTTYFQ RVLIFILLTAVAPSMT >C22 FHLTTRGGEPHMIVSKQERGKSLLFKTSTGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIAFFLAHAIGTSITQ KGIIFILLMLVTPSMA >C23 FHLTTRGGEPHMIVSKHERGKALLFKTSTGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C24 FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIVFILLMLVTPSMA >C25 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLVAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C26 FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSRTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C27 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDAWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C28 FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTVT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTYFQ RVLIFILLTAVAPSMT >C29 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTMIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C30 FHLTSRDGEPHMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGERRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C31 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPQITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGTIFILLMLATPSMA >C32 FHLTSRNGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C33 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILANTIGTTHFQ RALIFILLTAVAPSMT >C34 FHLTTRGGEPHMIVGKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C35 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMA >C36 FHLTTRNGEPHMIVSMQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C37 FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTAPGDHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTYFQ RVLILILLTAVAPSMT >C38 FHLTSRDGEPRMIVGKNERGKTLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C39 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRREKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIAFFLAHAIGTSITQ KGIIFILLMLVTPSMA >C40 FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFAIMAAILAYTIGTTHFQ RVLIFILLTAVAPSMT >C41 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPQITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIAFFLAHAIGTSITQ KGIIFILLMLVTPSMA >C42 FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTVMAAILAYTIGTTYFQ RVLIFILLTAVAPSMT >C43 FHLTTRGGEPHMIVGKQERGKSLLFKTSAGVNMCTLIAMDLGELCDDTMT YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C44 FHLTSRDGEPRMIVGKNERGKSLLFKTATGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSAWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLIQ KVVIFILLMLVTPSMT >C45 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPQITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVVAFFLAHAIGTSITQ KGIIFILLMLVTPSMA >C46 FHLTTRNGEPHMIVGIQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAVILAYTIGTTHFQ RVLIFILLTAVAPSMT >C47 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFTLLMLVTPSMT >C48 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YRCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFTLLMLVTPSMT >C49 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVAIAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C50 FHLTSRDGEPRMIVGKNERGKSLLFKTATGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLIQ 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]