gotoh

Name	gotoh JSON
Version	0.1.6 JSON
	download
home_page	https://github.com/rbturnbull/gotoh
Summary	Sequence Alignment with different penalties for opening gaps and extending them.
upload_time	2025-02-11 22:03:58
maintainer	None
docs_url	None
author	Robert Turnbull
requires_python	<3.12,>=3.8
license	Apache-2.0
keywords	multiple sequence alignment
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            # gotoh

![pipline](https://github.com/rbturnbull/gotoh/actions/workflows/pipeline.yml/badge.svg)

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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