Comprehensive suite of molecular biology and sequence analysis tools

Unlock the value of your sequence data

Geneious Prime makes bioinformatics accessible by transforming raw data into visualizations that make sequence analysis intuitive and user-friendly.

Sanger Sequencing Analysis

Simple sequence assembly and easy editing of contigs. Automatic annotation for gene prediction, motifs, translation, and variant calling.

Genotype microsatellite traces with automated ladder fitting and peak calling and generate tables of alleles.

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.

Molecular Biology

Simulate molecular cloning in one step including Gateway, Golden Gate and In-Fusion cloning.

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

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

NGS Pre-Processing, Assembly and Mapping

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

Reliable reference mapping with exclusive mapping algorithms and flexible de novo genome assembly with alignment tools available for comparison and finishing.

Alignment and Phylogenetics

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.


Rapidly search all key databases at NCBI for literature, DNA and protein sequence information. Submit sequences directly to GenBank.

BLAST search against sequences in NCBI databases or set up a local database and BLAST it locally.

What’s New in Geneious Prime 2023?

Highlights include primer specificity testing, cloning validation, STAR RNA-seq mapper, and CRISPR improvements.

Discover all of the brand new features, improvements, and enhancements in Geneious Prime 2023.

The backbone of your scientific research

Data Management

Increase process efficiency and improve collaboration with intuitive folder-based organization and a seamlessly integrated shared database. Simple drag and drop for import and export of a large number of common file formats including GenBank, SnapGene and FASTQ.


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.


Create your own automated workflows or use in-built workflows to increase efficiency and reduce human error. Automate external database searches to continuously receive the latest information on genomes, sequences, and protein structures.


We care a great deal about finding new ways to get science done faster and more efficiently. Our development team works constantly throughout the year to ensure Geneious Prime runs beautifully and there’s always a new release around the corner.

See Geneious Prime in Action

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Geneious is an absolutely beautiful package to work with. We love it and we are telling everyone about it.
Charles MooreNovartis Pharma AG, Switzerland

Geneious Prime has you covered

Explore a list of the comprehensive set of molecular biology and sequence analysis tools available in Geneious Prime
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 
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
  • 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 TopHat
  • De novo assembly algorithms including Geneious, SPAdes, Flye, MIRA, Tadpole and Velvet
  • Learn more about mapping and de novo assembly 
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 
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 
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 
  • Build trees with Geneious tree builder, MrBayes, PAUP*, PhyML, RAxML and more
  • Visualize, edit and markup your trees
  • Interactive distance matrix viewer
  • Publication quality export
  • Learn more about phylogenetic tree building 
Microsatellite Analysis
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
  • 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 
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 
Data Management and Collaboration
  • Drag and drop import of files and folders, including Vector NTI databases
  • 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
Searching and BLAST
  • Direct access to NCBI public BLAST databases
  • Custom BLAST for private local databases
  • 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 
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