---
name: "t_coffee"
section: "1"
platform: "linux"
package: "t-coffee"
version: "13.45.0.4846264+really13.41.0.28bdc39+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/t_coffee"
---

# t\_coffee(1)

multiple sequence alignment

## 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)](/clustalw/1.md), **/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).