๐Ÿงฌ Multiple Sequence Alignment

Clustal Omega Multiple Sequence Alignment

An implementation conforming to the Clustal Omega algorithm. Supports guide tree construction via mBed clustering, HMM-profile-profile progressive alignment, and iterative refinement. Uses BLOSUM62. All sequence data is processed locally in the browser.

๐Ÿ“ฅ Sequence Input
Sequence Type
Sequences: 0   Max length: โ€”
โš™๏ธ Parameter Settings
Guide Tree Construction
Clustering Method
mBed Seeds
mBed: Fast O(N log N) clustering. Effective for large sequence sets. Seeds=0 for auto (โˆšN seeds).
Profile Alignment Parameters
Gap Open Penalty
Gap Extension Penalty
Weight Matrix
Use Sequence Weights
Clustal Omega always uses BLOSUM62 as the base matrix. Gap parameters are applied to the profile-profile dynamic programming step.
Iteration
Iterations
Iteration Strategy
Iterative refinement: rebuilds the guide tree and re-runs alignment. May take time on large datasets.
Output
Output Format
Display Width
Terminal Gap Correction
๐Ÿ“Š Analysis Summary
๐Ÿ”ฌ Alignment Results
๐Ÿ“ Sequence Identity Matrix (%)
๐ŸŒณ Guide Tree (mBed/NJ)
Tree layout
Branch lengths are based on the pairwise distance matrix. Embedded distances are used when mBed clustering is applied.
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