--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sun Jul 15 08:12:26 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/prM_2/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/DNG_N3/prM_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/prM_2/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/prM_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -4089.71 -4133.68 2 -4093.82 -4145.88 -------------------------------------- TOTAL -4090.38 -4145.19 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/DNG_N3/prM_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/prM_2/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/prM_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 6.256631 0.218353 5.308318 7.118173 6.250634 1092.31 1111.22 1.000 r(A<->C){all} 0.053237 0.000105 0.034694 0.073880 0.052431 706.18 736.29 1.001 r(A<->G){all} 0.199200 0.000548 0.151929 0.244180 0.198138 477.60 521.86 1.000 r(A<->T){all} 0.060935 0.000134 0.039696 0.084341 0.060294 818.85 883.38 1.001 r(C<->G){all} 0.019355 0.000058 0.004797 0.034151 0.018733 774.74 813.98 1.000 r(C<->T){all} 0.618362 0.000889 0.557423 0.673259 0.619681 537.62 567.28 1.001 r(G<->T){all} 0.048910 0.000126 0.027608 0.071390 0.048346 889.01 899.08 1.001 pi(A){all} 0.295509 0.000224 0.267760 0.326134 0.295298 936.95 972.40 1.000 pi(C){all} 0.249203 0.000179 0.222872 0.275124 0.248947 940.49 962.92 1.000 pi(G){all} 0.243668 0.000219 0.213374 0.271035 0.243664 704.06 773.44 1.000 pi(T){all} 0.211620 0.000143 0.187435 0.233256 0.211514 615.59 767.69 1.001 alpha{1,2} 0.200044 0.000290 0.166208 0.233081 0.199009 1354.50 1400.39 1.001 alpha{3} 3.527098 0.636081 2.081358 5.051661 3.432241 1470.84 1485.92 1.000 pinvar{all} 0.042199 0.000734 0.000023 0.091544 0.038666 1136.50 1236.84 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 -3834.413152 Model 2: PositiveSelection -3834.413152 Model 0: one-ratio -3857.943389 Model 3: discrete -3806.637188 Model 7: beta -3807.737171 Model 8: beta&w>1 -3807.737395 Model 0 vs 1 47.060473999999886 Model 2 vs 1 0.0 Model 8 vs 7 4.4799999977840343E-4
>C1 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCDDTMT YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C2 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C3 FHLTTRNGEPHMIVSRQEKGKSLLFKTENGVNMCTLMAMDLGELCEDTIT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWVLRHPGFTIMAAILAYTIGTTYFQ RVLIFILLTAVAPSMT >C4 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGERRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C5 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YRCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFTLLMLVTPSMT >C6 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRAQTWMSAEGAWRQVEKVETWAFRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C7 FHLTTLGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C8 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C9 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSVTQ KGIIFILLMLVTPSMA >C10 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWNQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C11 FHLTTRNGEPHMIVSIQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C12 FHLTTRNGEPHMIVSRQEKGKSLLFKTENGVNMCTLMAMDLGELCEDTIT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWVLRHPGFTIMAAILAYTIGTTYFQ RVLIFILLTAVAPSMT >C13 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLVAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C14 FHLTTRNGEPHMIVSRQEKGKSLLFKTENGVNMCTLMAMDLGELCEDTIT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWVLRHPGFTIMAAILAYTIGTTYFQ RVLIFILLTAVTPSMT >C15 FHLTSRDGEPRMIVGKNERGKSLLFKTATGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLIQ KVVIFILLMLVTPSMT >C16 FHLTTRGGEPHMMVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHTIGTSITQ KGIIFILLMLVTPSMA >C17 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCDDTMT YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C18 FHLTTRNGEPHMIVSIQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C19 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C20 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C21 FHLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVT YKCPLLVNTEPEDIDCWCNLTSAWVMYGTCTQSGERRREKRSVALTPHSG MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ RTVFFILMMLVAPSYG >C22 FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTLMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C23 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCDDTMT YKCPQISETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLLLVTPSMA >C24 FHLTTRNGEPHMIVGIQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ RVLIFILLTAVAPSMT >C25 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C26 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRAQTWMSAEGAWRQIEKVETWAFRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C27 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C28 FHLTTRGGEPHMVVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C29 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C30 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITETEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVTALFLAHVIGTSITQ KGIIFILLMLVTPSMA >C31 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C32 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C33 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C34 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C35 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C36 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGEFCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFMVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C37 FHLTTRNGEPHMIVGIQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ RVLIFILLTAVAPSMT >C38 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C39 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C40 FHLTSRDGEPRMIVAKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFVLLMLVTPSMT >C41 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITETEPDDVDCWCNATETWVTYGTCSQAGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSoo >C42 FHLTTRNGEPHMIVSRQEKGKSLLFKTENGVNMCTLMAMDLGELCEDTIT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWVLRHPGFTIMAAILAYTIGTTYFQ RVLIFILLTAVAPSMT >C43 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPQITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C44 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGEFCEDTMT YKCPRISEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C45 FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHTIGTSITQ KGIIFILLMLVTPSMA >C46 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C47 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCATTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C48 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C49 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C50 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA 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