📥 Sequence Input
Sequence type
Sequences: 0 Max length: —
⚙️ Parameter Settings
Pairwise Alignment Parameters
For FAST/APPROXIMATE:
K-tuple (word) size
Window size
Gap Penalty
Number of Top Diagonals
Scoring Method
For SLOW/ACCURATE:
Gap Open Penalty
Gap Extension Penalty
Weight Matrix
Multiple Alignment Parameters
Gap Open Penalty
Gap Extension Penalty
Weight Matrix
Weight Transition
Transition Weight
Hydrophilic Gaps
Hydrophilic Residues for Proteins
Output
Output Format
Display Width
Terminal gap correction
Turn OFF to approximate KEGG ClustalW behavior (terminal gaps are treated as ordinary gaps).
📊 Analysis Summary
🔬 Alignment Results
📐 Sequence Identity Matrix (%)
🌳 Guide Tree (Neighbor-Joining)
Tree layout
Branch length is based on the pairwise distance matrix used for the guide tree. Rooted view shows the guide-tree root at the left in a rectangular layout; unrooted view places the same branch lengths radially.
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