Metadata-Version: 2.1
Name: gotoh
Version: 0.1.2
Summary: Sequence Alignment with different penalties for opening gaps and extending them.
Home-page: https://github.com/rbturnbull/gotoh
License: Apache-2.0
Keywords: multiple sequence alignment
Author: Robert Turnbull
Author-email: robert.turnbull@unimelb.edu.au
Requires-Python: >=3.8,<4.0
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Dist: numpy (>=1.23.3,<2.0.0)
Project-URL: Repository, https://github.com/rbturnbull/gotoh
Description-Content-Type: text/markdown

# 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.
