--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sun Jul 15 00:52:53 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_1/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/DNG_N3/prM_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/prM_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/prM_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -4343.83 -4391.13 2 -4339.96 -4391.16 -------------------------------------- TOTAL -4340.63 -4391.15 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/DNG_N3/prM_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/prM_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/prM_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} 6.383840 0.240188 5.487246 7.380999 6.361173 544.12 860.14 1.001 r(A<->C){all} 0.041943 0.000074 0.026136 0.059278 0.041470 792.30 826.26 1.000 r(A<->G){all} 0.228902 0.000661 0.180308 0.279235 0.227874 540.73 582.32 1.001 r(A<->T){all} 0.066089 0.000131 0.044289 0.088642 0.065377 729.62 786.67 1.000 r(C<->G){all} 0.030782 0.000062 0.015186 0.044841 0.030162 964.16 982.26 1.002 r(C<->T){all} 0.591811 0.000946 0.533791 0.653417 0.592733 545.66 594.32 1.002 r(G<->T){all} 0.040474 0.000104 0.021768 0.061056 0.040035 842.72 942.25 1.000 pi(A){all} 0.297790 0.000220 0.267255 0.325573 0.297698 922.99 947.08 1.000 pi(C){all} 0.254520 0.000180 0.229634 0.281214 0.254402 872.52 936.17 1.000 pi(G){all} 0.236472 0.000193 0.207711 0.262222 0.235885 555.35 761.92 1.000 pi(T){all} 0.211218 0.000150 0.187994 0.236050 0.210679 768.33 819.21 1.000 alpha{1,2} 0.217617 0.000391 0.180970 0.257763 0.216413 1228.85 1364.92 1.000 alpha{3} 3.699540 0.687758 2.294604 5.448467 3.597695 1361.36 1389.00 1.000 pinvar{all} 0.059306 0.000896 0.000931 0.113201 0.057723 1302.31 1401.66 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 -4140.447938 Model 2: PositiveSelection -4140.447933 Model 0: one-ratio -4166.802614 Model 3: discrete -4105.581355 Model 7: beta -4107.374786 Model 8: beta&w>1 -4106.512007 Model 0 vs 1 52.70935199999985 Model 2 vs 1 9.999999747378752E-6 Model 8 vs 7 1.7255580000000919
>C1 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C2 FHLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVT YKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKRSVALTPHSG MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ RTVFFVLMMLVAPSYG >C3 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C4 FHLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVT YKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKRSVALTPHSG MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ RTVFFVLMMLVAPSYG >C5 FHLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVT YKCPLLVNTEPEDIDCWCNLTSAWVMYGTCTQSGERRREKRSVALTPHSG MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ RTVFFILMMLVAPSYG >C6 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITETEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C7 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFIILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C8 FHLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVT YKCPLLVNTEPEDIDCWCNLTSAWVMYGTCTQSGERRREKRSVALTPHSG MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ RTVFFILMMLVAPSYG >C9 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFAIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C10 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C11 FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDIDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C12 FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C13 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIAFFLAHAIGTSITQ KGIIFILLMLVTPSMA >C14 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C15 FHLTTRGGEPHMIVSKQERGKSLLFKTSVGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C16 FSLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVT YKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKRSVALTPHSG MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ RTVFFVLMMLVAPSYG >C17 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPQITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIAFFLAHAIGTSITQ KGIIFILLMLVTPSMA >C18 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPQITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C19 FHLTTRNGEPHMIVSRQEKGKSLLFKTENGVNMCTLMAMDLGELCEDTIT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWVLRHPGFTIMAAILAYTIGTTYFQ RVLIFILLTAVAPSMT >C20 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C21 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPHDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C22 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C23 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLKQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C24 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSCEGAWKQIQKVEIWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C25 FHLTTRNGEPHMIVGIQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWVLRHPGFTIMAAILAYTIGTTHFQ RVLIFILLTAVAPSMT >C26 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C27 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C28 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C29 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGEFCEDTMT YKCPRISEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C30 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWITYGTCSTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C31 FHLTTRGGEPHMIVGKQERGKSLLFKTSAGVNMCTLIAMDLGELCDDTMT YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C32 FHLTTRNGEPHMIVSRQEKGKSLLFKTENGVNMCTLMAMDLGELCEDTIT YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWVLRHPGFTIMAAILAYTIGTTYFQ RVLIFILLTAVTPSMT >C33 FHLTSRDGEPGMIVGKNERGKSIFFKTASGINMCTLIAMDLGEMCDDTVT YKCPFIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFVLLMLVTPSMA >C34 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCATTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ RALIFILLTAVAPSMT >C35 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILANTIGTTHFQ RALIFILLTAVAPSMT >C36 FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTLMAAILAYTIGTTNFQ RALIFILLTAVAPSMT >C37 FHLTTRNGEPHMIVGIQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ RVLIFILLTAVAPSMT >C38 FHLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVT YKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKRSVALTPHSG MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ RTVFFVLMMLVAPSYG >C39 FHLTTRGGEPHMIVGKQERGKSLLFKTSAGVNMCTLIAMDLGELCDDTMT YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHVIGTSITQ KGIIFILLMLVTPSMA >C40 FHLTTRNGEPHMIVSRQDKGKSLLFKTKDGTNMCTLMAMDLGELCEDTIT YKCPFLKQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ RVLIFILLTAVAPSMT >C41 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C42 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWAFRHPGFTVLALFLAHFIGTSLTQ KVVIFILLMLVTPSMT >C43 FHLTTRGGEPPMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C44 FHLTARGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGEFCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C45 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C46 FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ KVVIFILLMLVTPSMT >C47 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C48 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRREKRSVALAPHVG LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ KGIIFILLMLVTPSMA >C49 FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHVQRIETWILRHPGFAIMAAILAYTIGTTHFQ KALIFILLTAVAPSMT >C50 FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTLMAAILAYTIGTTNFQ RALIFILLTAVAPSMT 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_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_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 Inpu