🧬 Multiple Sequence Alignment

MAFFT Multiple Sequence Alignment

A simple browser-based multiple sequence alignment tool inspired by the GenomeNet MAFFT interface. The implemented methods are limited to two modes, Fast progressive and Accurate progressive, with the actual calculation steps shown below. Sequence data are processed only in your browser.

📥 Sequence Input
Sequence Type
Sequences: 0   Max length: —
⚙️ Parameter Settings
Alignment Settings
Algorithm mode
Scoring matrix
Gap opening penalty
Gap extension penalty
Output order
Output
Output Format
Display Width
📊 Analysis Summary
🔬 Alignment Results
📐 Pairwise identity matrix（%）
🌳 Guide tree（Neighbor-Joining）
Tree layout
Branch length is based on the pairwise distance matrix used for the guide tree. Rooted view places the guide-tree root at the left in a rectangular layout. Unrooted view arranges the same branch lengths radially.
🖥 Sequence comparison analysis with the GeneQuick app

You can perform and save Sanger sequence analysis and sequence comparisons. GenBank format is also supported.

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