API & Developers

Extend Geneious Prime with your own plugins or workflows

The Geneious Prime Plugin Development Kit allows anyone to start extending Geneious Prime with their own functionality:

  • Add your favorite algorithm, database or visualization to Geneious Prime
  • Write a plugin for your own command line program and let Geneious Prime take care of the front-end for you
  • Create a top secret plugin that gives your researchers an edge over the competition

Wrap Up a Command Line Program

If you have an existing command-line program that you want to run from inside Geneious Prime you might be able to use the graphical wrapper plugin creator to do that without writing any code.

Download Wrapper Plugin Creator

Install the above plugin in Geneious Prime and use Create/Edit Wrapper Plugin in the File menu to get started. Our RAxMLGarli and FastTree plugins were created this way.

Automate Your Analysis

Workflows are another great way to tailor Geneious Prime. In addition to all of the built-in workflow components, you can write small snippets of Java code to perform custom steps. This is a great way to begin coding tools in Geneious.

Workflows are built into Geneious Prime under the Tools menu or in the toolbar.

Develop Like a Pro

If you are a capable Java developer and you want to have complete control over your creation then the dev kit has everything you need. Most of the premium functionality built in to Geneious Prime is created with the same API.

Getting Started Guide

Java API Documentation

Download Plugin Development Kit

Download old development kits: R6 R7 R8 R9 R10 R11 2019 2020

Learn By Example

The dev kit contains many example plugins which are easy to build from or you can check out what developers like you have already created.

Browse open source projects

Browse all plugins


If you need guidance on extending and integrating Geneious Prime, please visit the knowledge base, ask our application support specialists or post on the Plugin Development Forum. For general Java questions, stackoverflow.com is your best friend.

For many years I’ve wanted a friendly, menu-driven interface to our Glimmer program, but my research group has never had the resources available to build one. The Geneious Glimmer interface is terrific; it will allow any scientist to find genes in almost any bacterial, viral, or archaeal sequence, without requiring background expertise in Unix command-line programs. I’m also very pleased that Geneious makes Glimmer available across multiple computer platforms, including Windows and Mac.
Prof. Steven SalzbergUniversity of Maryland