FASTA splitter

Split large FASTA files by sequence count or export individual files for each sequence.

Input

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What is FASTA Splitter?

FASTA Splitter divides multi-sequence FASTA files into smaller, manageable pieces. This is useful when downstream tools have sequence limits, when you need to parallelize analysis across multiple files, or when organizing sequences for batch processing.

Many bioinformatics tools restrict the number of sequences per submission. Instead of manually copying sequences into separate files, this tool automates the splitting process while preserving headers and sequence integrity.

How does FASTA Splitter work?

The tool parses your input FASTA file, identifies individual sequences by their header lines (starting with >), and distributes them into output files according to your chosen split mode.

All processing happens in your browser—your sequences are never uploaded to a server. The tool generates a ZIP archive containing all split files, ready for download.

Inputs & settings

Splitting options

Split mode: Determines how sequences are distributed across output files. Split by sequence count groups a fixed number of sequences per file. Individual files creates one file per sequence. Split by line treats each line as a separate file (rarely needed).
Sequences per file: When using Split by sequence count mode, this controls how many sequences go into each output file.

File naming

Output files need consistent, predictable names for downstream automation.

Naming convention: Choose between Numbered (part_001, part_002), Sequential (file_1, file_2), or Header-based (uses the first sequence's header as the filename).
File prefix: Custom prefix added to all output filenames.

Output options

Include summary file: Generates a text file listing how many sequences ended up in each output file.
Preserve original headers: Keeps FASTA headers unchanged. Disable only if you need simplified headers.

Understanding the results

The tool produces a ZIP archive containing:

Split FASTA files: Each file contains the sequences according to your split settings
Summary file (optional): A text file documenting the split statistics—total sequences, files created, and sequences per file

File extensions match your input (.fasta, .fa, or .fas).

Common use cases

Scenario	Recommended settings
Preparing for AlphaFold (1 sequence per job)	Split mode: `Individual files`
Batch processing with 100-sequence limit	Split mode: `Split by sequence count`, Sequences per file: `100`
Organizing sequences by identity	Split mode: `Individual files`, Naming: `Header-based`

Best practices

We recommend keeping Preserve original headers enabled unless you have a specific reason to modify them. Header information often contains identifiers needed to trace results back to source sequences.

For large files with hundreds of sequences, Numbered naming provides cleaner organization than Header-based, which can produce long or problematic filenames from complex headers.