needleEMBOSS Needle performs a global sequence alignment using the Needleman-Wunsch algorithm. It aligns two sequences (protein or nucleotide) end-to-end, optimizing the overall similarity score based on a substitution matrix and gap penalties.Versions

v6.6.0 (default)

Tags: sequence alignment, Needleman-Wunsch, EMBOSSParameters

asequence (file) required: First input sequence file for alignment.

bsequence (file) required: Second input sequence file for alignment.

gapopen (float): Penalty for opening a gap.

gapextend (float): Penalty for extending a gap.

endopen (float): Penalty for opening a terminal gap.

endextend (float): Penalty for extending a terminal gap.

format (enum): Alignment output format (pair, fasta, markx10, etc.). Options: pair, fasta, markx10, markx3, markx0

Links

Home page

Publication (DOI)

License: GPL-3.0

Cite as: Rice, P., Longden, I., and Bleasby, A. (2000). EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics, 16(6), 276–277.

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