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Multiple Sequence Alignment by MAFFT


CLUSTALW MAFFT PRRN

Multiple sequence alignment by MAFFT v6.864

Basic settings

Input:
Paste protein or DNA sequences in fasta format


or upload a file:

Advanced settings

Output order:
Same as input
Aligned
Strategy:
Moderately accurate (FFT-NS-2, FFT-NS-i or L-INS-i; depends on data size)
FFT-NS-1 (Very fast; progressive method)
FFT-NS-2 (Fast; progressive method)
(Medium; iterative refinement method, two cycles only)
FFT-NS-i (Slow; iterative refinement method)
L-INS-i (Very slow; probably most accurate; recommended for <200 sequences)
G-INS-i (Very slow; suitable for sequences of similar lengths; recommended for <200 sequences)
E-INS-i (Very slow; suitable for sequences containing large unalignable regions; recommended for <200 sequences)
Parameters:
Scoring matrix (for amino acid sequences):
Gap opening penalty: (1.0-3.0)
Offset value: (0.0-1.0; functions like gap extension penalty)
mafftE (aligns input sequences together with their homologues collected from SwissProt by BLAST):
On
Show collected homologues also (if any)
Number of homologues: (5-200)
Threshold: (1e-5 - 1e-40)

KEGG GenomeNet Kyoto University Bioinformatics Center