BioJava 3.* release

BioJava 3 is a major re-write of BioJava 1. The cookbook for the new API is available from here: . The content on this page is still available to support the legacy code base, which is now available through the biojava-legacy project on Github at [<>](

BioJava 1 reference

If you use BioJava 1 please cite:

BioJava In Anger - A Tutorial and Recipe Book for Those in a Hurry

BioJava can be both big and intimidating. For those of us who are in a hurry there really is a whole lot there to get your head around. This document is designed to help you develop BioJava programs that do 99% of common tasks without needing to read and understand 99% of the BioJava API.

The page was inspired by various programming cookbooks and follows a “How do I…?” type approach. Each “How do I?” is linked to some example code that does what you want and sometimes more. Basically if you find the code you want and copy and paste it into your program you should be up and running quickly. I have endeavoured to over document the code to make it more obvious what I am doing so some of the code might look a bit bloated.

If you have any suggestions, questions or comments contact the biojava mailing list. To subscribe to this list go here

If you re-use code from the cookbook please cite:


You can now read BioJava in Anger in French (Translated by Sylvain Foisy; mise à jour / updated : 28 décembre 2009).

You can also read Biojava in Anger in Portuguese (Translated by Dickson Guedes)

You can also read BioJava in Anger in Japanese (Translated by Takeshi Sasayama and Kentaro Sugino, updated 14 Aug 2004).

How about simplified Chinese? (Translated by Wu Xin).

And lets not forget this new Italian translation (translated by Alessandro Cipriani; last update: 9 Sep 2010).

How Do I….?


Alphabets and Symbols

Basic Sequence Manipulation



Sequence I/O


Locations and Features


Counts and Distributions

Weight Matrices and Dynamic Programming

User Interfaces

BioSQL and Sequence Databases

External Applications and Services

Genetic Algorithms

Protein Structure

Since BioJava 1.8, all protein structure modules have moved to BioJava3.


Cloud computing


This code is generously donated by people who probably have better things to do. Where possible we test it but errors may have crept in. As such, all code and advice here in has no warranty or guarantee of any sort. You didn’t pay for it and if you use it we are not responsible for anything that goes wrong. Be a good programmer and test it yourself before unleashing it on your corporate database.

The documentation on this site is the property of the people who contributed it. If you wish to use it in a publication please make a request through the biojava mailing list.

The code is open-source. A good definition of open-source can be found here. If you agree with that definition then you can use it.