Extract text from Sequence alignment files (ALN)
To convert ALN Alignment files to another format, you need Clustal or other Data software.
To convert other file formats to the "Bioinformatics Alignment File" file type, you need software like Clustal or a similar tool.
The .ALN file format is primarily a Multiple Sequence Alignment file. It stores plain text representations of aligned DNA, RNA, or protein sequences, complete with gap insertions and conservation symbols. It is heavily used in bioinformatics for phylogenetic tree construction and evolutionary analysis. A secondary, rarer use is for LinPro structural analysis data.
These files are typically generated by the Clustal family of programs (ClustalW, ClustalX, Clustal Omega). Users can open these files with tools like Jalview, BioEdit, or the EMBOSS suite.
Because .ALN is a plain text format specifically formatted for visual inspection, it is not always machine-readable for automated downstream processing scripts. It includes headers, whitespace mapping, and conservation scoring (asterisks) that easily break strict parsers in R or Python. You cannot easily merge or manipulate them in a standard spreadsheet without heavily breaking the alignment structure.
To use the sequences in standard programming libraries (like Biopython), convert .ALN to FASTA. For phylogenetic analysis, convert to .NEXUS (NEX) or .PHYLIP (PHY). If you simply want to view the data without specialized software, convert to TXT.
Convert.Guru analyzes your ALN file, detects the exact format, and lets you read the text inside.
Users also converted ALN-CLUSTAL_NUM, ALN-FASTA, ALN-CLUSTALW, PRALN, OUT, CZI, FASTA, BIN, PDF, ZIP and DND files.
If you want to convert ALN file to FASTA, you can use Clustal or similar software from the "Sequence Alignment Storage" category. In the File menu, look for Save As… or Export….
To convert files to ALN, try Clustal or another comparable tool in the "Sequence Alignment Storage" category.
The history of Convert.Guru began over 25 years ago in California with Tom Simondi’s file-format database. A former contributor to Space Shuttle development and a software pioneer of the 1980s, Simondi established a trusted resource for file type analysis that was even referenced by Microsoft Windows XP. Today, we use modern technology to process and convert thousands of file formats while continually improving our ALN converter.