Simple Sequence Aligners

This repo contains simple Java implementations of famous sequence alignment algorithms.

The implementations you see here were not built for speed, but rather simplicity and should be used as a learning tool for familiarizing yourself with alignment algorithms.

Algorithms that are implemented include the Needleman & Wunsch global alignment algorithm and the Smith & Waterman local alignment algorithm.

All implementations use the BLOSUM62 matrix by default.

Instructions

For example, to compile the local alignment algorithm, use the following command: javac LocalAlign.java

To then execute the program, use the following command and follow the printed instructions: java LocalAlign

Notes

All implementations tested using OpenJDK 1.8 on Windows and Linux