---
name: "seaview_align.sh"
section: "1"
platform: "linux"
package: "seaview"
version: "20021127-4"
release: "Debian 3.1 (Sarge)"
platforms: ["linux"]
url: "https://new.carta.tech/seaview"
---

# seaview\_align.sh(1)

a multiple sequence alignment editor

Part of [seaview(1)](/seaview/1.md).

## NAME

seaview - a multiple sequence alignment editor

## SYNOPSIS

**seaview** *\[options\] \[filename\]*

## DESCRIPTION

This manual page documents briefly the **seaview**, command. This manual page was written for the Debian GNU/Linux distribution because the original program does not have a manual page. Instead, it has online documentation, see below.

**seaview** is a graphical multiple sequence alignment editor. SeaView is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE, NEXUS). It allows one to manually edit the alignment, and also to run DOT-PLOT or CLUSTAL programs to locally  improve the alignment.

## OPTIONS

- **-save \<format\_name\>**

  format\_name, either mase, clustal, phylip, msf, fasta, or nexus, sets the  default file format for saving operations

- **-fast**

  sequences will be displayed faster but less smoothly

- **-inverted**

  residues will appear as black letters on a colored background

## ARGUMENT

"filename" is an optional alignment file to be loaded. The expected format for this file is that of the default format for saving operations.

## SEE ALSO

The program is fully documented online. Press the "help" button in the main window.

## AUTHOR

This manual page was written by Stephane Bortzmeyer \<bortzmeyer@debian.org\>, for the Debian GNU/Linux system (but may be used by others).