A tutorial for the alignment module of BioJava.

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.

This tutorial is split into several chapters.

Chapter 1 - Quick Installation

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

The content of this tutorial is available under the CC-BY license, available here.

BioJava 5: A community driven open-source bioinformatics library
Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte
PLOS Computational Biology (2019) 15 (2):e1006791.

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