Geneious Prime Plugins

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

Write Your Own Plugins 

The Geneious Plugin Development Kit (PDK) allows you to take advantage of the Geneious Prime API to write your own plugins or workflows


Multiple sequence alignment using the latest addition to the Clustal family.
André Marques
Align large genomes using LASTZ
Fast and accurate multiple sequence alignment with MAFFT
Align multiple genomes to identify large-scale evolutionary events using Mauve
Aaron Darling
Partition allele multisets from multiple alignments
Jed Barlow


Adapter/Quality Trimming and Filtering
Fast and sensitive aligner for RNA and DNA
Reference mapping with Bowtie
Perform contig assembly using CAP3
Sorts sequences in a contig according to the position of their first non-gap base.
Biomatters Ltd.
Merge paired sequencing reads using FLASH
Dave O'Connor
A de novo assembler for single molecule sequencing reads, such as PacBio and Oxford Nanopore
A versatile mapper / pairwise aligner for genomic and spliced nucleotide sequences
Efficient and accurate sequence assembly with MIRA
Fast splice junction mapping for RNA-Seq reads with TopHat
De novo assembly of short reads with Velvet

Nucleotide Analysis

Eukaryotic gene prediction with Augustus
Michael Thon
Complement or Reverse DNA sequences without doing both
Find targets for DNA methylation by predicting CpG islands
Tobias Thierer
Find existing CRISPR sites in bacteria and archaea
Dr Chris Duran
Predict transcription factors and protein coding regions
Haplotype based variant finding with FreeBayes.
Predict genes in microbial DNA with Glimmer
Identify heterozygotes in chromatograms with secondary peak calling
Streamlined microsatellite genotyping
Automatically mutate or shuffle sequences
Search genomes for tandem repeats / microsatellites using Phobos
Dr Christoph Mayer
Find polymorphic tandem repeats in alignments using Phobos
Lars Smits
Find large, distant repeats


Fast maximum-likelihood tree building on large datasets with RAxML
Fast phylogenetic tree building of huge datasets
Bayesian phylogenetic analysis using MrBayes
Prof. Marc Suchard
Phylogenetic inference using PAUP* 4.0
Phylogenetic inference for molecular evolution using PhyML
Identify recombination events in phylogenetic history with DualBrothers
Prof. Marc Suchard
Assess putative species in phylogenetic trees
Brad Masters et al.

Protein Analysis

Predict protein coiled coil regions
Tobias Thierer
Predict secondary structure, antigenic regions and signal cleavage sites.
Automatically annotate proteins with InterPro domains
Michael Thon
Structural alignment of PDB protein sequences
Predict transmembrane spanning regions of proteins
Prof. Marc Suchard

Services and Searching

Integrated laboratory information management system for DNA barcoding
Search and download eukaryotic pathogen genes
List the size of all folders in your local database
Simplified submission of sequences, genomes, features, primers and traces.
Jump to documents by entering their unique IDs
Opens a terminal window inside Geneious for scripting in the Groovy language
Taxonomically classify samples against your own database of known sequences