Geneious Prime

Molecular Biology and Sequence Analysis Tools

Geneious Prime puts industry-leading bioinformatics and molecular biology tools directly into researchers hands, streamlining sequence analysis and insights.

Powerful, Intuitive Sequence Analysis

Sanger Sequencing analysis

Improve your mapping accuracy and decrease your analysis time with simple sequence assembly and easy editing of contigs.

Easily identify, examine and resolve disagreements with powerful SNP detection and variant calling.

Next Generation Sequencing Analysis

Beautiful visualizations of annotated genomes and assemblies displayed in a highly customizable sequence view.

Powerful SNP variants analysis, simple RNA-Seq expression analysis and amplicon metagenomics.

NGS Pre-Processing, Assembly and Mapping

Ensure accurate downstream analysis with extensive NGS pre-processing tools producing clean sequence data.

Reliable reference mapping for short or long reads with exclusive mapping algorithms and flexible de novo genome assembly.


Perform pairwise and multiple alignments of DNA or protein using trusted algorithms, including MAFFT and Clustal Omega.


Build phylogenetic trees using peer-reviewed algorithms, including RAxML and PAUP*, and adjust display settings.

Faster, More Accurate Molecular Biology


Simulate low and high throughput cloning experiments including Golden Gate, Gateway, Gibson, Restriction and Parts Cloning.

Validate your cloning with a visual tool for automating sequence alignment during batch plasmid validation.

Primer Design

Design and test PCR and sequencing primers, and create your own searchable primer database.

Be confident your primers will only bind in a single location with automatic identification of any additional, off target, binding sites.


Powerful CRISPR tools make it easy to find specific sites, design guide RNAs and analyze your editing results.

Annotate and Predict

Automatically annotate a new genome based on existing patterns and annotations in public or local databases. Transfer annotations by similarity or using an alignment.

Real time prediction of DNA translations, consensus sequences, DNA and protein sequences.

Microsatellite Analysis

Genotype microsatellite traces with automated ladder fitting and peak calling. Generate tables of alleles and export for further analysis.

The Backbone of Your Scientific Research

Geneious Cloud

Work in Geneious Cloud where all of your data, notes and processes are readily accessible to your peers in a secure, access controlled way.

Add data to the familiar folder structure of the cloud workspace from within Geneious Prime to start collaborating.

Convert File Formats

Simple drag and drop for import and export of a large number of common file formats including GenBank, SnapGene, Excel and FASTQ.


BLAST search against sequences in NCBI databases or set up a custom database and BLAST it locally. Submit sequences directly to GenBank.

Automate external database searches to continuously receive the latest information on genomes, sequences, and protein structures.

Automated Workflows

Create your own automated workflows or use in-built workflows to increase efficiency and reduce human error.

Command Line Interface

Sync data and run Geneious Prime operations and workflows locally, or execute on more powerful servers.

Customization & Plugins

Extend the functionality of Geneious Prime with our collection of plugins available for assembly, alignment, phylogenetics and more. Integrate with existing systems and add your own custom algorithms using a highly interoperable API.

Geneious Prime Has You Covered

Explore a list of the comprehensive set of molecular biology and sequence analysis tools available in Geneious Prime

Mapping and de novo Assembly

  • Simply switch between industry leading algorithms for mapping and de novo assembly
  • Support for assembly of Sanger and NGS data, including Illumina, PacBio and Oxford Nanopore reads of any length, including paired-end reads and hybrid assemblies
  • Algorithm advisors to help you choose the best algorithm
  • Produce circular contigs when assembling microbial genomes, plasmids and other circular sequences
  • Genome comparison and finishing with MAUVE genome alignment
  • Mappers including Geneious, Geneious for RNA Seq, BBMap, Minimap2, Bowtie2 and STAR
  • De novo assembly algorithms including Geneious, SPAdes, Flye, MIRA, Tadpole and Velvet
  • Learn more about mapping and de novo assembly

Molecular Cloning

  • View plasmid maps, automatically annotate vectors, and copy-paste sequences with annotations
  • One-step GoldenGate (Type IIS) and Restriction cloning
  • Homology-based cloning including Gibson, GeneArt, and In-Fusion
  • TOPO cloning
  • Parts cloning
  • Cloning validation
  • Parent/descendant lineage tracking of cloning operations
  • Codon optimization and back translation
  • Silent mutation analysis to find potential restriction sites to introduce
  • CRISPR gDNA design
  • Simulated PCR, digestion and ligation
  • Learn more about cloning

Sequence Analysis

  • Trim, assemble, and view Sanger sequencing trace files
  • Correct base calls and create consensus sequences
  • Annotate motifs, ORFs and repeats
  • Predict genes and structural elements
  • Real-time annotation via similarity search against database
  • Translate selections on the fly, or show translation for annotations or selected frame
  • Dynamic graphs and statistics for sequence properties such as pI, molecular weight, melting point, AA composition and more
  • Learn more about Sanger sequence analysis

Primer Design

  • Automatically design PCR and sequencing primers and hybridization probes, to any target region or entire sequence
  • Easily add primers in the Sequence View
  • Design basic and degenerate PCR primers
  • Add and remove extensions to a primer sequence before, during or after the design process
  • Primer specificity testing to check for additional binding sites on the template sequence
  • Screen for physical properties, hairpins and primer-dimers
  • Drag and drop your primers in FASTA, spreadsheet or GenBank format
  • Learn more about primer design

NGS Pre-Processing

  • Import Illumina, PacBio and NanoPore reads
  • Trim, filter and demultiplex both single-end and paired-end data
  • Merge paired reads
  • De-duplicate
  • Error correct and normalize
  • Filter out chimeras
  • Learn more about NGS pre-processing

Data Management and Collaboration

  • Drag and drop import of files and folders, including Excel sheets
  • Import metadata from a spreadsheet onto sequences and other documents
  • Smart NGS import – one step import of any assortment of SAM, BAM, GFF, BED, and VCF files
  • Intuitive folder-based project organization
  • Seamlessly integrated shared database
  • Rapid search against all sequences and metadata in your database
  • Extensive export options
  • Learn more about data management

Variant Calling and Expression Analysis

  • Call SNPs/variants using Geneious or FreeBayes
  • Perform real-time filtering of tabular results with synchronized genome view
  • Calculate and compare expression levels on mapped RNA-seq data
  • Visualize using PCA and volcano plots
  • Learn more about NGS analysis

Searching and BLAST

  • Direct access to NCBI public BLAST databases
  • Custom BLAST for private local databases
  • Annotate by BLAST
  • Integrated search of external databases including GenBank and UniProt
  • Upload your sequences directly to GenBank
  • Search for literature in PubMed
  • Advanced searching against your local or shared database
  • Learn more about searching and BLAST

Sequence Alignment

  • Multiple and pairwise sequence alignment of DNA or protein including full genome alignment
  • Align with trusted algorithms including Geneious Aligner, MUSCLE, MAFFT, Clustal Omega, MAUVE and LastZ
  • View and edit alignments with real-time translation and highlighting
  • Learn more about alignment

Automated Workflows

  • Create workflows for automated bulk analysis using a visual editor
  • More than 20 in-built workflows for performing pipelines including Apply Variants to Reference Sequence, Map Reads then find SNPs, and Randomly Sample Sequences
  • Extend capabilities with option to write custom code workflows
  • Learn more about workflows


API & Developers

  • Add specialized functionality or integrate with other systems using the Plugin Development Kit
  • Add your favorite algorithm, database or visualization
  • Wrap a command line program to run via the Geneious Prime GUI
  • Learn more about plugin development

Microsatellite Analysis

"I have found Geneious to be one of the most intuitive and powerful sequence analysis programs that I have used in all my years working in the molecular biology field. Thanks for making my life so much easier."
Prof. John Payne
University of California
Get started with Geneious today