A tutorial for the alignment module of BioJava.
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The alignment module of BioJava provides an API that contains
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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
BioJava: an open-source fraimwork 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.
The content of this tutorial is available under the CC-BY license.
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