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 						       T-COFFEE(1)