Sequence Alignment with different penalties for opening gaps and extending them.
Project description
gotoh
Performs a global sequence alignment (Needleman-Wunsch) with affine gap penalties (Gotoh). It returns a tuple with the number of characters that match, mismatch, open gaps and extend gaps. The scores/penalties are given as arguments and the defaults correspond to the basic Levenshtein distance.
It can also produce a multiple sequence alignment.
Based on Brent Pedersen’s nwalign which was originally posted at https://bitbucket.org/brentp/biostuff/ but now has disappeared.
For more information, see chapter 7 of Robert Turnbull's thesis 'The Textual History of Codex Sinaiticus Arabicus and its Family'.
Documentation and code clean up to come.
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