Online Multiple Alignment Tool

Align multiple biological sequences (DNA, RNA, proteins) with configurable parameters and downloadable results.

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About This Tool

This online multiple sequence alignment tool allows researchers and students to align multiple biological sequences (DNA, RNA, or protein) using a progressive alignment algorithm. Upload sequences in FASTA format or paste them directly, configure alignment parameters like gap penalty and match score, and get professionally formatted alignment results with similarity scores. The tool implements the Needleman-Wunsch algorithm for pairwise alignment and progressive alignment for multiple sequences, providing accurate biological sequence analysis.

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How to Use

Enter sequences in FASTA format in the text area or upload a FASTA file.
Configure alignment parameters (gap penalty, match score, mismatch penalty).
Click 'Align Sequences' to process.
View the aligned sequences with color-coded matches and similarity scores.
Download results as FASTA, CLUSTAL, or plain text.

Frequently Asked Questions

Find Quick Answers

What sequence formats are supported?

The tool supports FASTA format. Each sequence should start with a '>' line containing the identifier, followed by the sequence on subsequent lines.

What alignment algorithm does this tool use?

It uses Needleman-Wunsch for pairwise alignment and progressive alignment (hierarchical clustering) for multiple sequences, which is standard for biological sequence alignment.

Can I align protein sequences?

Yes, the tool works with DNA, RNA, and protein sequences. The scoring matrix automatically adjusts based on sequence type detection.

How many sequences can I align at once?

The tool can handle up to 50 sequences of reasonable length (up to 10,000 characters each) for optimal performance.

Need to run multiple calculations?

Create a free account today to unlock unlimited daily runs, access advanced parameters, save your history, and request custom features.

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