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URL: http://github.com/biojava/biojava-tutorial/tree/master/alignment

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README.md

The BioJava - Alignment Module

A tutorial for the alignment module of BioJava.

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

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

License

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

Please cite

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.
doi pubmed

Navigation: Home | Book 2: The Alignment Module

Prev: Book 1: The Core Module

Next: Book 3: The Structure Modules
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