API & Customization

Customize, automate and integrate Geneious Prime to increase efficiency in your organization

Plugin Development Kit

The Geneious Public API allows you to create a wide variety of plugins to extend functionality, integrate with existing systems and add your own custom algorithms. The Dev Kit allows capable Java developers to have complete control over their plugin creation.

To get started read the plugin development Getting Started Guide, the Java API Documentation, browse previous Open Source Projects and current Geneious Plugins, then download the Dev Kit.

Download Plugin Development Kit

For previous versions of the development kit contact us

Command Line Interface

Run Geneious Prime operations and workflows as part of your broader bioinformatic pipelines locally or execute on more powerful servers.

Sync data from your pipelines directly into (or out of) your Geneious Prime local or shared databases.

Read Chapter 21 in the User Manual for more information on using the Command Line Interface.

Wrapper Plugin Creator for Command Line Programs

Use the graphical wrapper plugin creator to run an existing command line program from inside Geneious Prime without writing any code. The Geneious RAxMLGarli and FastTree plugins were created this way.

Download Wrapper Plugin Creator

Install the above plugin in Geneious Prime and use Create/Edit Wrapper Plugin in the File menu to get started.

Add Custom Code to Workflows

Workflows allow you to automate your analysis and to customize Geneious Prime. In addition to all of the built-in workflow components, you can write snippets of Java code to perform custom steps.

Custom code allows you to create Geneious operations that do almost anything. The Workflow custom code automatically inserts the surrounding import statements for the complete Geneious API and a class framework around the methods you implement.



Plugin Development Getting Started Guide

Everything you need to know to get started creating plugins

Plugin Development Knowledge Base

Guidance on extending and integrating Geneious Prime

Plugin Development Forum

Post questions to other users developing plugins

General Java Questions

For general Java questions, is your best friend.



Extend the functionality of Geneious Prime with plugins for assembly, alignment, phylogenetics and more.

Open Source Plugin Projects

Check out what plugins previous developers have created.


Create and share automated workflows

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