Geneious Prime

Geneious Prime is a comprehensive suite of molecular biology and bioinformatics tools designed for researchers working with protein, Sanger, and next-generation sequencing data. Developed by Geneious, the platform brings together industry-leading sequence analysis, cloning, primer design, CRISPR, phylogenetics, and data management capabilities into a single, intuitive interface — streamlining workflows and accelerating scientific insights for molecular biologists across academia and industry.

The platform is built to support the full research lifecycle, from raw sequence data import and pre-processing through to assembly, annotation, variant calling, and publication-quality output. Geneious Prime is suitable for individual researchers and collaborative teams alike, offering both desktop functionality and cloud-based data management.

Sanger Sequencing Analysis

• Trim, assemble, and view Sanger sequencing trace files with simple contig editing
• Correct base calls and create consensus sequences
• Powerful SNP detection and variant calling to identify, examine, and resolve disagreements
• Annotate motifs, ORFs, and repeats; predict genes and structural elements
• Real-time annotation via similarity search against a database
• Translate selections on the fly, or display translation for annotations or selected frames
• Dynamic graphs and statistics for sequence properties including pI, molecular weight, melting point, and amino acid composition

Next-Generation Sequencing (NGS) Analysis

• Beautiful, highly customizable visualizations of annotated genomes and assemblies
• Powerful SNP and variant analysis using Geneious or FreeBayes variant callers
• Simple RNA-Seq expression analysis with PCA and volcano plot visualizations
• Amplicon metagenomics support
• Perform real-time filtering of tabular results with a synchronized genome view
• Calculate and compare expression levels on mapped RNA-seq data

NGS Pre-Processing, Assembly, and Mapping

• Import Illumina, PacBio, and Oxford Nanopore reads of any length, including paired-end reads
• Trim, filter, demultiplex, merge paired reads, de-duplicate, error correct, normalize, and filter chimeras
• Support for hybrid assemblies and circular contig production for microbial genomes and plasmids
• Mappers including Geneious, Geneious for RNA-Seq, BBMap, Minimap2, Bowtie2, and STAR
• De novo assembly algorithms including Geneious, SPAdes, Flye, MIRA, Tadpole, and Velvet
• Algorithm advisors to help select the best approach for each dataset
• Genome comparison and finishing with MAUVE genome alignment

Sequence Alignment

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

Phylogenetics

• Build phylogenetic trees using peer-reviewed algorithms including Geneious tree builder, MrBayes, PAUP*, PhyML, and RAxML
• Visualize, edit, and mark up trees with adjustable display settings
• Interactive distance matrix viewer
• Publication-quality export of tree graphics

Molecular Cloning

• Simulate low and high throughput cloning experiments including Golden Gate (Type IIS), Gateway, Gibson, GeneArt, In-Fusion, TOPO, Restriction, and Parts Cloning
• View plasmid maps, automatically annotate vectors, and copy-paste sequences with annotations
• Cloning validation with a visual tool for automating sequence alignment during batch plasmid validation
• 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

Primer Design

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

CRISPR

• Find specific target sites and design guide RNAs with powerful CRISPR tools
• Analyze editing results directly within the platform
• CRISPR gDNA design integrated into the cloning workflow

Annotation and Prediction

• Automatically annotate new genomes 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, and DNA and protein sequences

Microsatellite Analysis

• Import raw ABI trace files
• Automated ladder fitting and peak calling; trim, predict, and manually adjust peaks
• Bin peaks into alleles and produce tabular output of allele calls
• Generate tables of alleles and export for further analysis

Searching and BLAST

• Direct access to NCBI public BLAST databases and support for custom BLAST against private local databases
• Annotate sequences by BLAST results
• Integrated search of external databases including GenBank and UniProt
• Upload sequences directly to GenBank
• Search for literature in PubMed
• Automate external database searches to continuously receive the latest information on genomes, sequences, and protein structures

Automated Workflows

• Create custom automated workflows using a visual editor for bulk analysis
• More than 20 in-built workflows including Apply Variants to Reference Sequence, Map Reads then Find SNPs, and Randomly Sample Sequences
• Extend capabilities with the option to write custom code workflows
• Sync data and run Geneious Prime operations and workflows locally or execute on more powerful servers via a Command Line Interface

Data Management and Collaboration

• Geneious Cloud Workspace for secure team collaboration and data backup
• Intuitive folder-based project organization with 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 SAM, BAM, GFF, BED, and VCF files
• Rapid search against all sequences and metadata in your database
• Extensive export options and simple drag-and-drop support for common file formats including GenBank, SnapGene, Excel, and FASTQ