BioJava comes with implementations of the Combinatorial Extension (CE) and FATCAT algorithms. Both algorithms come in two variations, as such one can say that BioJava supports the following four algorithms.

1. Combinatorial Extension (CE)

2. Combinatorial Extension with Circular Permutation (CE-CP)

3. FATCAT - rigid

4. FATCAT - flexible.

Before going the details how to use the algorithms programmatically, let's take a look at the user interface that cames with the *biojava-structure-gui* module.

<pre>

AlignmentGui.getInstance();

</pre>

shows this user interface:


The Combinatorial Extension (CE) algorithm was originally developed by [Shindyalov and Bourne in 1998](http://peds.oxfordjournals.org/content/11/9/739.short).

Thanks to P. Bourne, Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute their algorithms.