A Java API for computation on permutations and sequences

Vincent A. Cicirello

About the JavaPermutationTools (JPT) API

The JavaPermutationTools (JPT) API provides Java classes that enable representing and generating permutations and sequences, as well as performing computation on permutations and sequences. This current release consists of implementations of a variety of permutation distance metrics as well as distance metrics on sequences (i.e., Strings, arrays, and other ordered data types). More computation on permutations and sequences will be added later.

The JPT source code repository is hosted on GitHub; and is licensed under the GNU General Public License Version 3 (GPLv3). The of JavaPermutationTools can be found on this site.

JPT is organized into the following packages:

In addition to the source code, the repository contains a folder of example programs that show basic usage of the API, as well as a folder of replication programs that reproduce results found in published papers. There are also JUnit test cases.

How to Cite

If you use this API in your research, please cite the following article which describes the library:

Related Publications

The following papers, most of which are related to fitness landscape analysis, used this API. Programs for replicating the data from these papers can be found in the replication directory. In order to fully understand the data generated by the programs in the replication directory, you may need to consult these papers: