All about A3M Files

The A3M file type is primarily associated with HH-suite.

A3M	File extension: A3M
	File type:	Multiple sequence alignment file

What is an A3M file?

A3M files mostly belong to HH-suite. A3M files are text files that store multiple sequence alignments of protein sequences. They list amino acids in aligned columns, where uppercase letters mark conserved positions and lowercase letters show insertions. This clear format is used by software like HMMER3, HH-suite (including HHblits and HHpred) and AlphaFold2 to study protein evolution and structure.
Key details provided by FilExt.com include:

Multiple Sequence Alignment: Aligns several protein sequences to reveal similarities and differences.

Protein Sequence Analysis: Helps create profiles used in structural and functional predictions.

Works within bioinformatics pipelines for advanced sequence comparisons.

For more info, visit HMMER, AlphaFold, HHblits or HHpred.

FilExt.com note: Users can open these files with standard text editors for a quick view or use dedicated bioinformatics tools for deeper analysis.

How to open A3M files

You need a suitable software like HH-suite to open an A3M file. Without proper software you will receive a Windows message "How do you want to open this file?" or "Windows cannot open this file" or a similar Mac/iPhone/Android alert. If you cannot open your A3M file correctly, try to right-click or long-press the file. Then click "Open with" and choose an application. You can also display a A3M file directly in the browser:. Just drag the file onto this browser window and drop it.

Online A3M Text Viewer

Choose your .a3m file to view

or drag and drop it here

Online File Viewer

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How to extract texts from A3M files or capture a screenshot to PDF, JPG, DOCX, TXT, ...

If you want to extract texts from A3M file or capture a screenshot, you can use our free Online A3M File Viewer:

To do so, click the "Choose your .a3m file to view" button above.
After your file is opened in browser,
click "Save as..." in the menu.
Then choose the file format (e.g. JPG, PDF, DOCX, TXT, ...) you want.
Your file will be converted and downloaded.

Programs that open and convert A3M files:

HH-suite
See the previous paragraphs to learn more about the main application. A3M files are often referred to as HH-suite data files because this type of file is primarily created or used by this software.
Authorware (Unpackaged Macintosh FIle) by Adobe Systems Incorporated
Authorware was a Macromedia product. Macromedia was taken over by Adobe.

A3M file format:

If you can determine the file format, the associated program can also be determined. A file format is determined by the file extension and signature, so JPEG images have the extension .jpg and the first bytes in the file are ÿØÿ. However, different programs can use the same file extension, and file extensions can be assigned incorrectly. So a detailed analysis of a file is vital in order to determine the format and the associated program. Our evaluation of the A3M files is as follows:

As a file extension, A3M isn't very common and is used by different programs with different formats. The following file formats are most commonly found in A3M files:

25% of all A3M files use the same file format, which can be identified by the letters ">101" at the beginning. These files contain text and words, not binary data. A3M files can be up to 15 MB in size, but are often around 14 KB - 5 MB. The file type is very recent. Examples of file names are bfd.mgnify30.metaeuk30.smag30.a3m or uniref.a3m. These files are attributed to metaeuk, mgnify, smag and pair.
10% of all A3M files use the same file format, which can be identified by the letters ">query" at the beginning. These files are plain text, which means they can be viewed with any text editor such as Windows Editor, Nano for Linux, and TextEdit for macOS. The files are 320 KB to 26 MB in size, with a median of 4 MB. The keywords >query are typical for these files. Such files sometimes refer to chains, fold, paired, unpaired and trim.

The remaining 65% of all A3M files are files with no common format, the following 11 formats exist: CADS and chain. Tagged as hits, uniclust, hhblits, protein, reduced or hhpred. You can get all the details of your A3M file by dragging it onto this page or by clicking the button "Choose your .a3m file to view" above.

Technical Data for A3M File Extension

File classification:

Data

Related files:

fasta, sto, clustal, msf, a2m, aln, am3, pdb, tgt, zip, a4m, aab, a4r

an a3m Multiple sequence alignment file is a special file format and should only be edited and saved with the appropriate software.

How to solve problems with A3M files

Associate the A3M file extension with the correct application.
Update your software that should actually open multiple sequence alignment files. Because only the current version supports the latest A3M file format. Search, therefore, e.g. on the manufacturer website after an available HH-suite update.
To make sure that your A3M file is not corrupted or virus-infected, get the file again and scan it with Google's virustotal.com.
Click here to open your .A3M file online - secure, fast, and no downloads needed.