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

# pair\_align(1)

Pairwise alignment

## NAME

pair\_align - Pairwise alignment

## SYNOPSIS

**pair\_align** \[*OPTIONS*\] **-s** *IN*

## DESCRIPTION

The program allows one to align two sequences using dyamic programming alignment algorithms while tweaking various parameters.

## OPTIONS

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

  Display the help message.

- **--version**

  Display version information.

### Main Options:

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

  FASTA file with two sequences. Valid filetypes are: *.frn*, *.fna*, *.ffn*, *.fasta*, *.faa*, and *.fa*.

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

  Sequence alphabet. One of *protein*, *dna*, *rna*, and *text*. Default: *protein*.

- **-m**, **--method** *STRING*

  DP alignment method: Needleman-Wunsch, Gotoh, Smith-Waterman, Longest Common Subsequence One of *nw*, *gotoh*, *sw*, and *lcs*. Default: *gotoh*.

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

  Output filename. Valid filetypes are: *.msf*, *.frn*, *.fna*, *.ffn*, *.fasta*, *.faa*, and *.fa*. Default: *out.fasta*.

### Scoring Options:

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

  Gap open penalty. Default: *-11*.

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

  Gap extension penalty. Default: *-1*.

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

  Score matrix.

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

  Match score. Default: *5*.

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

  Mismatch penalty. Default: *-4*.

### Banded Alignment Options:

- **-lo**, **--low** *INTEGER*

  Lower diagonal.

- **-hi**, **--high** *INTEGER*

  Upper diagonal.

### DP Matrix Configuration Options:

- **-c**, **--config** *STRING*

  Alignment configuration. One of *ffff*, *ffft*, *fftf*, *fftt*, *ftff*, *ftft*, *fttf*, *fttt*, *tfff*, *tfft*, *tftf*, *tftt*, *ttff*, *ttft*, *tttf*, and *tttt*.

## ALIGNMENT CONFIGURATION

The alignment configuration is a string of four characters, each being either t or f. All combinations are allowed. The meaning is as follows.

- tfff

  First row initialized with 0s.

- ftff

  First column initialized with 0s.

- fftf

  Search last column for maximum.

- ffft

  Search last row for maximum.