Plugins extend the functionality of Geneious by providing specialized analysis and additional data sources.
InstallationThe easiest way to install plugins is directly from within Geneious by selecting Tools -> Plugins... from the menu.
Create your ownYou can write your own plugins for Geneious including viewers, databases, sequence operations and more using our free Java Plugin Development Kit
Streamlined microsatellite genotyping. Call peaks, bin them and produce a table of genotypes to export for further analysis.
2012 iEvoBio Geneious Challenge Plugins
Winner: PlasmoDB and PiroplasmaDB
Search and download gene and protein information on eukaryotic pathogens.
Created by Charles Ma.
Runner Up: QuRE
Viral quasispecies reconstruction from next-generation sequencing data.
Created by Mattai Prosperi, Marco Salemi and Tyler Strickland
Supercomputing / Services
DeCypher - 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.
Moorea Biocode Plugins
Genbank Submission Plugin
Geneious now supports uploading your sequences directly to GenBank. Simplify the process of submitting sequences, genomes, features, primers, traces, and more!
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.
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.
Maximum Likelihood tree building for alignments. Please cite these papers when using PHYML.
Explore species properties on a phylogenetic tree, including the chance probability of distinctive clades and the reliability of species identification.
DNA Sequence Analysis
Glimmer Gene Prediction
Predict genes using Glimmer – a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
Mauve Genome Alignment
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.
A nucleotide sequence graph for predicting CpG islands based on the model and parameterisation described by Richard Durbin, Sean Eddy et al. (1999).
Identifies heterozygotes in sequences with trace information by looking at the relative height of traces at peak positions.
Phobos - A Tandem Repeat Search Tool
Phobos detects perfect and imperfect microsatellites, minisatellites and DNA-satellites in whole genomes with a high accuracy. Phobos is freely available for non-commercial use.
Complement or Reverse Only
Provides actions to reverse a sequence without complementing it and to complement without reversing.
Protein Sequence Analysis
Annotate protein sequences by searching InterPro, an integrated database of protein signatures. Plugin by Michael Thon.
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.
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.
Predicts transmembrane spanning regions of proteins using TMHMM (Transmembrane Hidden Markov model).
PDB Structure Aligner
Aligns two PDB structures using BioJava structure alignment (Requires Geneious 4.8)