README.md

SimplePairwiseAlignment

This repository contains a simple implementation of a pairwise alignment algorithm for FASTA files using the Needleman-Wunsch algorithm.

Table of Contents

• Features
• Requirements
• Installation
• Usage
• License

Features

• Reads sequences from FASTA files
• Aligns sequences using the Needleman-Wunsch algorithm
• Outputs aligned sequences to the console and a file

Requirements

• CMake 3.10 or higher
• C++11 or higher

Installation

1. Clone the repository:

   git clone https://github.com/yourusername/SimplePairwiseAlignment.git
   cd SimplePairwiseAlignment

2. Create a build directory and navigate to it:

   mkdir build
   cd build

3. Generate the build files using CMake:

   cmake ..

4. Build the project using make:

   make

Usage

1. Run the executable:

   ./PairwiseAlignment

2. View the output:

   • The aligned sequences will be printed to the console.
   • The aligned sequences will be saved in aligned_sequences.txt in the build directory.

License

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