Sequence Toolkit
DNA & RNA analysis · Rust compiled to WebAssembly
Connecting…
Analyze
Composition · GC · reverse complement
GC window
Sliding GC content & skew
Align
Global & local pairwise
Tree
Distances · UPGMA · Newick
Sequences
Load example
FASTA or plain sequence
Drop a .fasta file
Multiple records are fine. IUPAC codes (N, R, Y…) and U for RNA are accepted.
Open file…
Analyze
Sequence
Load example
FASTA or plain sequence
Drop a .fasta file
Window (bp)
Step (bp)
Each window reports GC content and GC skew = (G − C) / (G + C). At most 10,000 windows per request.
Open file…
Plot
Pairwise alignment
Global example
Local example
Global
Needleman-Wunsch
Local
Smith-Waterman
Sequence A
Sequence B
Match
Mismatch
Gap
Ctrl
+
Enter
to run
Align
Sequences
Load example
FASTA, 2–30 records with unique ids
Drop a .fasta file
Every pair is aligned globally (Needleman-Wunsch), then the distances are clustered with UPGMA.
p-distance
fraction of sites that differ
Jukes-Cantor
corrected for multiple hits
Match
Mismatch
Gap
Gaps are skipped when counting differences, so keep the gap penalty well above the mismatch penalty. Otherwise the aligner can hide differences behind gaps.
Open file…
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