Metadata-Version: 2.4
Name: gotoh
Version: 0.2.0
Summary: Sequence Alignment with different penalties for opening gaps and extending them.
License: Apache-2.0
License-File: LICENSE
Keywords: multiple sequence alignment
Author: Robert Turnbull
Author-email: robert.turnbull@unimelb.edu.au
Requires-Python: >=3.9,<3.15
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Dist: numpy (>=1.23.3)
Project-URL: Homepage, https://github.com/rbturnbull/gotoh
Project-URL: Repository, https://github.com/rbturnbull/gotoh
Description-Content-Type: text/x-rst

gotoh
=====

.. start-badges

|pypi badge| |testing badge|

.. |pypi badge| image:: https://img.shields.io/pypi/v/gotoh?color=blue
    :target: https://pypi.org/project/gotoh/

.. |testing badge| image:: https://github.com/rbturnbull/gotoh/actions/workflows/pipeline.yml/badge.svg
    :target: https://github.com/rbturnbull/gotoh/actions

.. end-badges

To install, run:

.. code-block:: bash

    pip install gotoh


This package 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.

Documentation and code clean up to come.

Credits
==================================

.. start-credits

`Robert Turnbull <https://robturnbull.com>`_

Based on Brent Pedersen's nwalign which was originally posted at
https://bitbucket.org/brentp/biostuff/ but now has disappeared.

For more information, see Robert Turnbull's book `Codex Sinaiticus Arabicus and Its Family <https://brill.com/display/title/69300>`_.

.. end-credits

