Unlock the value of your sequence data
Sequence Analysis and Genomics
User-friendly, intuitive interface packed full of essential genomics tools for Sanger, NGS and long read sequence analysis, including pairwise and multiple alignments, de novo assembly, mapping, expression analysis, variant calling, NGS visualization, sequence and chromatogram analysis, automatic annotation, and phylogenetic tree building.
Molecular Biology
Perform a wide-range of cloning and primer design operations within one interface. Automatically annotate plasmid maps and expression vectors. Simulate a variety of molecular cloning operations including restriction cloning, Gibson Assembly, Gateway cloning and TOPO cloning. Design and test primers, find CRISPR sites, and optimize codons.
Data Management
Simply drag and drop to import, export and convert your sequences, annotations and notes in common file formats including Genbank, SnapGene, FASTQ, FASTA, BAM, VCF, GFF, or import your complete Vector NTI database. Arrange and browse your data library how you like with document filtering, batch renaming, and document history automatically saved. Available for Mac, Windows and Linux.
The backbone of your scientific research
Automate
Create your own automated workflows or use in-built workflows to increase efficiency, control business processes, and reduce human error in your research. Connect directly to databases including UniProt, NCBI (Entrez), BLAST and PubMed. Databases searches can be automated, allowing you to continuously receive the latest information on genomes, sequences, and protein structures.
Collaborate
Transform data management across teams, increase process efficiency and improve collaboration with intuitive folder-based organization and a seamlessly integrated shared database. Geneious Server Database is also available to purchase with a greater level of control and increased security for data access for your organization over the standard shared database.
Customize
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
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
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
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
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
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
Phylogenetics
- 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
Microsatellite Analysis
- Import raw ABI trace files
- Trim, predict and manually adjust peaks
- Bin peaks into alleles
- Produce tabular output of allele calls
- Learn more
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
- Simulated PCR, digestion and ligation
- CRISPR site finder
- Learn more
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
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
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
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
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
Take the First Step
Discover how Geneious tools and services can help you simplify and empower sequencing research and analysis.