t-coffee(1) multiple sequence alignment

SYNOPSIS

t_coffee [options]file

t-coffee aligns multiple DNA or protein sequences.

OPTIONS

A summary of options is included below. For a complete description, see the documentation.
-full_log S [0]
-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]
-seq S [0]
-in S [0] Mlalign_id_pair Mslow_pair
-pdb S [0]
-out_lib W_F [0] no
-lib_only D [0] 0
-outseqweight W_F [0] no
-seq_source S [0] ANY
-cosmetic_penalty D [0] -50
-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
-usetree R_F [0]
-tree_mode S [0] slow
-quicktree FL [0] 0
-outfile W_F [0] default
-maximise FL [1] 1
-output S [0] clustalw
-infile R_F [0]
-matrix S [0] blosum62mt
-tg_mode D [0] 1
-profile_mode S [0] cw_profile_profile
-profile_comparison S [0] full50
-dp_mode S [0] cfasta_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
-type S [0]
-outorder S [0] aligned
-seqnos S [0] off
-case S [0] keep
-cpu D [0] 0
-maxnseq D [0] 60
-maxlen D [0] -1
-weight S [0] default
-seq_weight S [0] t_coffee
-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
-evaluate_mode S [0] 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
-profile S [0]
-profile1 S [0]
-profile2 S [0]
-extend_matrix FL [0] 0
-prot_min_sim D [40] 40
-prot_max_sim D [60] 60
-prot_min_cov D [0] 0
-pdb_min_sim D [30] 30
-pdb_max_sim D [100] 100
-pdb_min_cov D [50] 50
-pdb_blast_server W_F [0] SIB
-prot_blast_server W_F [0] SIB
-pdb_db W_F [0] nrl3d
-protein_db W_F [0] nr
-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
-msa_mode S [0] tree
-lalign_n_top D [0] 10
-iterate D [0] 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
-seq_to_keep S [0]
-dpa_master_aln S [0]
-dpa_maxnseq D [0] 10
-dpa_min_score1 D [0]
-dpa_min_score2 D [0]
-dpa_keep_tmpfile FL [0] 0
-dpa_debug D [0] 0
-multi_thread S [0]
-lib_list S [0]

AUTHOR

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).