Plugins
Plugins extend Geneious's functionality by providing specialized analysis and additional data sources. Anyone can write plugins using our freely available Public API – in fact, most of Geneious's standard functionality is developed using this API.
The following programs come built into Geneious Pro (no plugin required): MUSCLE, ClustalW, BLAST, Primer3, VecScreen and Jmol.
All of the plugins below are freely downloadable but may require Geneious Pro. Pro only plugins can be used with a Pro trial.
Instructions
If you have Geneious 3.7 or higher, you can install plugins directly from within Geneious by selecting Tools -> Plugins... from the menu in Geneious.
In older versions, download the plugin file below then select Tools -> Preferences... and choose Install Plugin... on the Plugins tab.
Supercomputing
DeCypher (Pro Only) - BETA
Use our simple graphical interface to run batch sequence searches on your TimeLogic DeCypher server from within Geneious. Requires a DeCypher accelerator card. This plugin is a beta release.
Green Button
Run your intensive analyses on a super-powerful computing grid. Requires a Green Button account.
Phylogenetics
PAUP* (Pro Only)
Run PAUP* phylogenetic inference from inside Geneious. You will need a licensed copy of PAUP* to use this plugin. Includes Modeltest (GPL).
PAUP* for Mac OS 9 is not supported. PAUP* licensees are entitled to upgrade to the OS X version of PAUP* for free. See the PAUP* website for more details.
MrBayes
Runs the well known program MrBayes (included) for Bayesian estimation of phylogeny. Includes interactive display of posterior output. MrBayes is a standalone application and can also be run independently of Geneious. It is released under the GNU General Public License, and its source code is freely available.
DualBrothers Recombination Detection
Detect recombination and spatial phylogenetic variation using the freely available program DualBrothers.
PHYML
Maximum Likelihood tree building for alignments. Please cite these papers when using PHYML.
DNA Sequence Analysis
Mauve Genome Alignment (Pro Only)
Construct and visualize multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Based on the freely available program Mauve.
CpG Islands (Pro Only)
A nucleotide sequence graph for predicting CpG islands based on the model and parameterisation described by Richard Durbin, Sean Eddy et al. (1999).
Heterozygotes Plugin
Identifies heterozygotes in sequences with trace information by looking at the relative height of traces at peak positions
Protein Sequence Analysis
EMBOSS Tools (Pro Only)
Run several EMBOSS programs (included) from within Geneious including back translate, mutate, shuffle, garnier secondary structure prediction and more: Program List. EMBOSS is a freely available software package for molecular biology.
Coiled Coils (Pro Only)
A protein sequence graph for predicting coiled-coil regions based on "Predicting coiled-coil regions in proteins", Andrei Lupas. Curr Opin Struct Biol. 1997 Jun;7(3):388-93.
Transmembrane Prediction
Predicts transmembrane spanning regions of proteins using TMHMM (Transmembrane Hidden Markov model).
Import/Export
Vector NTI Import (Pro Only)
Import files created by Vector NTI including molecule, oligo and citation archives as well as sequences (.gb/.gp) and alignments (.apr).
- This plugin is included with Geneious 3.6+
Create your own plugins
You can write your own plugins for Geneious including viewers, databases, sequence operations and more using our free public API for Java.
Download the Geneious API and documentation
NOTE: Plugins developed with this version of the API will only be compatible with Geneious 3.8 and above.