---
name: "seqan_tcoffee"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "2.4.0+dfsg-16"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/seqan_tcoffee"
---

# seqan\_tcoffee(1)

Multiple sequence alignment

## NAME

seqan\_tcoffee - Multiple sequence alignment

## SYNOPSIS

**seqan\_tcoffee** -s \<*FASTA FILE*\> \[*OPTIONS*\]

## DESCRIPTION

SeqAn::T-Coffee is a multiple sequence alignment tool.

(c) Copyright 2009 by Tobias Rausch

## OPTIONS

- **-h**, **--help**

  Display the help message.

- **--version**

  Display version information.

### Main Options::

- **-s**, **--seq** *INPUT\_FILE*

  Name of multi-fasta input file. Valid filetypes are: *.frn*, *.fna*, *.ffn*, *.fasta*, *.faa*, and *.fa*.

- **-a**, **--alphabet** *STRING*

  The used sequence alphabet. One of *protein*, *dna*, *rna*, and *iupac*. Default: *protein*.

- **-o**, **--outfile** *OUTPUT\_FILE*

  Name of the output file. Valid filetypes are: *.msf*, *.frn*, *.fna*, *.ffn*, *.fasta*, *.faa*, and *.fa*. Default: *out.fasta*.

### Segment Match Generation Options::

- **-m**, **--method** List of *STRING*'s

  Defines the generation method for matches. To select multiple generation methods recall this option with different arguments.  One of *global*, *local*, *overlap*, and *lcs*. Default: *global* and *local*.

- **-l**, **--libraries** List of *INPUT\_FILE*'s

  Name of match file. To select multiple files recall this option with different arguments. Valid filetypes are: *.mums*, *.lib*, *.blast*, and *.aln*.

- **-pa**, **--pairwise-alignment** *STRING*

  Pairwise alignment method. Default: *unbanded* for usual alignments (\< 50 sequences), *banded* for deep alignments (\>= 50 sequences) One of *unbanded* and *banded*.

- **-bw**, **--band-width** *INTEGER*

  Band width. This option automatically select *banded* pairwise alignment (see **pa** for details) In range \[2..inf\]. Default: *60*.

### Scoring Options::

- **-g**, **--gop** *INTEGER*

  gap open penalty Default: *-13*.

- **-e**, **--gex** *INTEGER*

  gap extension penalty Default: *-1*.

- **-ma**, **--matrix** *STRING*

  score matrix Default: *Blosum62*.

- **-ms**, **--msc** *INTEGER*

  match score Default: *5*.

- **-mm**, **--mmsc** *INTEGER*

  mismatch penalty Default: *-4*.

### Guide Tree Options::

- **-u**, **--usetree** *STRING*

  Name of the file containing the *Newick Guide Tree*.

- **-b**, **--build** *STRING*

  Method to build the tree. Following methods are provided: *Neighbor-Joining* (**nj**), *UPGMA single linkage* (**min**), *UPGMA complete linkage* (**max**), *UPGMA average linkage* (**avg**), *UPGMA weighted average linkage* (**wavg**). *Neighbor-Joining* creates an unrooted tree, which we root at the last joined pair. One of *nj*, *min*, *max*, *avg*, and *wavg*. Default: *nj*.

### Alignment Evaluation Options::

- **-i**, **--infile** *INPUT\_FILE*

  Name of the alignment file \<*FASTA FILE*\> Valid filetypes are: *.frn*, *.fna*, *.ffn*, *.fasta*, *.faa*, and *.fa*.