T-COFFEE(1)

💖 T-COFFEE 💖

okay bestie so we're in the General Commands Manual and this is the page for t-coffee — yes, the T-COFFEE(1) page, you know the one. sit down, grab a strawberry 🍓, this is a long one and it's so worth it.

🌸 NAME 🌸

t-coffee — multiple sequence alignment.

that's the whole job description. multiple sequence alignment. iconic. 👑

🦋 SYNOPSIS 🦋

t_coffee [options]file

bestie I need you to look at that line very carefully. there is no space between [options] and file. that's not me being lazy, that's literally how the manpage has it. I kept it char-for-char 💅

t-coffee aligns multiple DNA or protein sequences. periodt. ✨

✨ OPTIONS ✨

A summary of options is included below. For a complete description, see the documentation. (fr fr — this list is the trailer, not the movie, the docs are where the plot lives 😭)

okay so real talk about the format: every line down there is the option, then a type tag, then a bracketed number, then the default. I'm keeping every single character of that exactly as the manpage wrote it — no guessing, no "fixing", no renaming. if it's S it stays S. if it's very_fast_triplet it stays very_fast_triplet. no cap. 🫶

• -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

not me pointing out that -split shows up twice in the original 💀 I did not merge them, I did not delete one, I did not "fix" it. both of them are right there. that's the manpage's business, not mine 🫶

• -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]

and that's all one hundred and three of them, bestie. yes I counted. yes I need a nap. 😭💖

👀 SEE ALSO 👀

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

go click around, the docs directory is right there on your own machine, local queen behaviour 🌈

🫶 AUTHOR 🫶

t-coffee was written by Cedric Notredame <cedric.notredame@europe.com> — absolute legend, main character energy, we stan. 💜

This manual page was written by Steffen Moeller <moeller@pzr.uni-rostock.de>, for the Debian project (but may be used by others). yes that's the real wording — "but may be used by others" — so go ahead, it's giving generous ✨

and that's the whole page, bestie 🎀 the manual name up top is T-COFFEE, it lives in the General Commands Manual, and the footer stamps it May 13, 2005 with the version-and-name tag T-COFFEE(1) on both ends. slay, we ate, and now you know all 103 of her little flags. go align something. 💅💖