pairwise_alignments_to_msa

Introduction

pairwise_alignments_to_msa is a Python package that converts pairwise tuple sequence alignments into a multi-sequence alignment (MSA).

This tool is useful in bioinformatics pipelines when you have aligned pairs of sequences (such as the output of progressive alignment algorithms or pairwise alignment steps) and want to generate a consistent multi-sequence alignment.

Installation

From PyPI

pip install pairwise_alignments_to_msa

From GitHub (development version)

git clone https://github.com/Cassiebastress/pairwise_alignments_to_msa.git
cd pairwise_alignments_to_msa
poetry install

Usage

Here is an example of how to use pairwise_alignments_to_msa:

from pairwise_alignments_to_msa.alignment import aligned_tuples_to_MSA

# Example list of aligned sequence pairs
tuple_alignments = [
    ["a-bcdef", "aAb----"],
    ["a-bcdef", "-Bbc-ef"],
    ["abcde-f-", "---deEfF"]
    # Add more aligned pairs as needed
]

msa = aligned_tuples_to_MSA(tuple_alignments)

# Print the resulting MSA
for seq in msa:
    print(seq)

Code of Conduct

This project adheres to the Contributor Covenant Code of Conduct.
Please review it before contributing.

History

0.1.0

• Initial release
• Core functionality: aligned_tuples_to_MSA for converting tuple sequence alignments into MSA

License

This project is licensed under the MIT License. See the LICENSE file for details.