t-coffee - multiple sequence alignment

       t-coffee was written by Cedric Notredame <cedric.notredame@europe.com>

       This manual page was written by Steffen Moeller <moeller@pzr.uni-rostock.de>, for the Debian project (but
       may be used by others).

                                                  May 13, 2005                                       T-COFFEE(1)

       t-coffee - multiple sequence alignment

       A summary of options is included below.  For a complete description, see the documentation.

       -full_logS[0]-run_nameS[0]-mem_modeS[0]mem-extendD[1]1-extend_modeS[0]very_fast_triplet-max_n_pairD[0]10-seq_name_for_quadrupletS[0]all-compactS[0]default-cleanS[0]no-do_selfFL[0]0-do_normaliseD[0]1000-template_fileS[0]-seqS[0]-inS[0]Mlalign_id_pairMslow_pair-pdbS[0]-out_libW_F[0]no-lib_onlyD[0]0-outseqweightW_F[0]no-seq_sourceS[0]ANY-cosmetic_penaltyD[0]-50-gapopenD[0]0-gapextD[0]0-fgapopenD[0]0-fgapextD[0]0-nomatchD[0]0-newtreeW_F[0]default-usetreeR_F[0]-tree_modeS[0]slow-quicktreeFL[0]0-outfileW_F[0]default-maximiseFL[1]1-outputS[0]clustalw-infileR_F[0]-matrixS[0]blosum62mt-tg_modeD[0]1-profile_modeS[0]cw_profile_profile-profile_comparisonS[0]full50-dp_modeS[0]cfasta_pair_wise-ktupleD[0]1-ndiagD[0]0-diag_thresholdD[0]0-diag_modeD[0]0-sim_matrixS[0]vasiliky-typeS[0]-outorderS[0]aligned-seqnosS[0]off-caseS[0]keep-cpuD[0]0-maxnseqD[0]60-maxlenD[0]-1-weightS[0]default-seq_weightS[0]t_coffee-alignFL[1]1-moccaFL[0]0-domainFL[0]0-startD[0]0-lenD[0]0-scaleD[0]0-mocca_interactiveFL[0]0-evaluate_modeS[0]t_coffee_fast-get_typeFL[0]0-clean_alnD[0]0-clean_thresholdD[1]1-clean_iterationD[1]1-clean_evaluate_modeS[0]t_coffee_fast-profileS[0]-profile1S[0]-profile2S[0]-extend_matrixFL[0]0-prot_min_simD[40]40-prot_max_simD[60]60-prot_min_covD[0]0-pdb_min_simD[30]30-pdb_max_simD[100]100-pdb_min_covD[50]50-pdb_blast_serverW_F[0]SIB-prot_blast_serverW_F[0]SIB-pdb_dbW_F[0]nrl3d-protein_dbW_F[0]nr-method_logW_F[0]no-struc_to_useS[0]-cacheW_F[0]use-align_pdb_param_fileW_F[0]no-align_pdb_hasch_modeW_F[0]hasch_ca_trace_bubble-msa_modeS[0]tree-lalign_n_topD[0]10-iterateD[0]0-trimD[0]0-splitD[0]0-trimfileS[0]default-splitD[0]0-split_nseq_thresD[0]0-split_score_thresD[0]0-check_pdb_statusD[0]0-seq_to_keepS[0]-dpa_master_alnS[0]-dpa_maxnseqD[0]10-dpa_min_score1D[0]-dpa_min_score2D[0]-dpa_keep_tmpfileFL[0]0-dpa_debugD[0]0-multi_threadS[0]-lib_listS[0]

clustalw(1), /usr/share/doc/t-coffee/,http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home

t_coffee [options]filet-coffee aligns multiple DNA or protein sequences.