Alignment Format Converter

Convert between multiple sequence alignment formats: FASTA, Clustal, PHYLIP, NEXUS, and Stockholm

What is Alignment Format Converter?

A tool to convert multiple sequence alignments between common bioinformatics formats including FASTA, Clustal, PHYLIP, NEXUS, and Stockholm. Essential for compatibility with different analysis software.

How to Use This Tool

  1. Paste or upload your alignment in any supported format
  2. Select desired output format from dropdown
  3. View converted alignment automatically
  4. Download or copy the result

Supported Formats

  • FASTA: Simple header + sequence format
  • Clustal: ClustalW/ClustalX output format
  • PHYLIP: Phylogenetic analysis format
  • NEXUS: Rich format with metadata
  • Stockholm: Pfam/Rfam database format

Example Input (FASTA)

>seq1 ATGCATGC--AT >seq2 ATGC--GCGCAT >seq3 ATGCATGCGCAT

Example Output (Clustal)

CLUSTAL format seq1 ATGCATGC--AT seq2 ATGC--GCGCAT seq3 ATGCATGCGCAT **** ** **

FAQ

Q: Which formats are supported?
A: FASTA, Clustal, PHYLIP, NEXUS, and Stockholm formats.

Q: Are gaps preserved during conversion?
A: Yes, gap characters (-) are maintained in all formats.