| T-COFFEE(1) | General Commands Manual | T-COFFEE(1) |
NAME¶
t-coffee - 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]
SEE ALSO¶
clustalw(1), /usr/share/doc/t-coffee/,
http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home
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).
| May 13, 2005 |