ALN File

What are ALN files and how to open them

Are you having problems opening an ALN file or are you simply curious about its contents? We're here to explain the properties of these files and provide you with software that can open or handle your ALN files.

What is an ALN file?

An .ALN file is a Clustal Alignment Format file.

Clustal Alignment Format is a plain-text format used to store the results of multiple sequence alignments produced by the Clustal family of programs (such as ClustalW, ClustalX, Clustal Omega). It shows aligned sequences (DNA, RNA, or protein) arranged together, helping users see where sequences match, differ, or have gaps. Its main purpose is to allow inspection of alignment and to serve as input for downstream tools that support this format.

Files in this format contain several sequences that have been aligned so that their residues (or nucleotides) are in columns. Gaps are represented by the hyphen character. Alongside the aligned sequences, a "conservation line" appears under each block of alignment: an asterisk (*) marks columns where all sequences have the same character, a colon (:) marks strongly similar substitutions, a period (.) marks weakly similar ones, and blanks indicate non-conserved positions. The sequences are shown in blocks, each block showing a fixed number of residues per line (often up to 60), with optional cumulative residue counts at the ends of lines.

The format begins with a header line that starts with the word CLUSTAL (such as "CLUSTAL W (2.1) multiple sequence alignment"), often followed by version or program name. After one or more blank lines, alignment data appear in interleaved blocks: each block lists each sequence by name, aligned residue segments, and optionally the residue count; then the conservation line; then blank lines before the next block.

Files in this format can be identified internally by the ASCII signature "CLUSTAL" at the start of the file and by the presence of the phrase "multiple sequence alignment" in the header.

How to open ALN files

Important: Different programs may use files with the ALN file extension for different purposes, so unless you are sure which format your ALN file is, you may need to try a few different programs.

While we have not verified the apps ourselves yet, our users have suggested six different ALN openers which you will find listed below.

Last updated: August 17, 2026

Various apps that use files with this extension

These apps are known to open certain types of ALN files. Remember, different programs may use ALN files for different purposes, so you may need to try out a few of them to be able to open your specific file.

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