The BioJava - Alignment Module ===================================================== A tutorial for the alignment module of [BioJava](http://www.biojava.org). ## About

The alignment module of BioJava provides an API that contains

Implementations of dynamic programming algorithms for sequence alignment
Reading and Writing of popular alignment file formats
A single-, or multi- threaded multiple sequence alignment algorithm.

## Index This tutorial is split into several chapters. Chapter 1 - Quick [Installation](installation.md) Chapter 2 - Global alignment - Needleman and Wunsch algorithm Chapter 3 - Local alignment - Smith-Waterman algorithm Chapter 4 - Multiple Sequence alignment Chapter 5 - Reading and writing of multiple alignments Chapter 6 - BLAST - why you don't need BioJava for parsing BLAST ## Please cite **BioJava: an open-source framework for bioinformatics in 2012**
*Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis*
[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract)
[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863) ## License The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license. [view license](../license.md) --- Navigation: [Home](../README.md) | Book 2: The Alignment module Prev: [Book 1: The Core module](../core/README.md) Next: [Book 3: The Protein Structure modules](../structure/README.md)