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.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for gotoh-0.1.4-cp310-cp310-macosx_13_0_x86_64.whl
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 046f3b1b9cf020419fce607943aaeb22b5a857fbe3a18da7593a1fa85bdc96c1 |
|
| MD5 | f24c65980901c2e845ae0c86b4af0c00 |
|
| BLAKE2b-256 | 8a438d911b1641d832c4851859ed79aff307447d4061191e52fdd3e2a479f756 |
