A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.
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jebl
LICENSE.md
Readme.md

Readme.md

Java Evolutionary Biology Library

A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.

Requirements

  • Java Development Kit 1.6+
  • Apache Ant

Installation

Run the following command from within the jebl directory:

ant dist

The built jebl.jar library in the dist folder can then be included in your project.

API Documentation

To produce the Javadoc in the doc directory run the following:

ant document

Development

This project includes three components:

  1. jebl
  2. org.virion.jam
  3. org.virion.jam.maconly

org.virion.jam.maconly that can only be built under Mac OS X. A pre-built version is located in the lib directory so it can be included on the classpath for non-Macs. If anything is changed in this package then it has to be built separately (see the -mac-only targets).

Operating System

If you are using an IDE and not on a Mac then you will need to exclude org.virion.jam.maconly in order to compile the project.

Contributing