Comprehensive suite of molecular biology and sequence analysis tools
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.
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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.
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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.
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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. Database searches can be automated, allowing you to continuously receive the latest information on genomes, sequences, and protein structures.
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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.
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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.
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Geneious Prime has you covered
A complete toolkit for every stage of your molecular biology and genomics workflow.
NGS Pre-Processing
- ›Import Illumina, PacBio and NanoPore reads
- ›Trim, filter and demultiplex paired-end data
- ›Merge paired reads and de-duplicate
- ›Error correct, normalize and filter chimeras
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, BBMap, Minimap2, Bowtie2 and TopHat
- ›De novo assembly algorithms including Geneious, SPAdes, Flye, MIRA, Tadpole and Velvet
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
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
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
Phylogenetics
- ›Build trees with MrBayes, PAUP*, PhyML, RAxML and FastTree
- ›Visualize, edit and mark up phylogenetic trees
- ›Interactive distance matrix viewer
- ›Publication-quality export of trees and alignments
Microsatellite Analysis
- ›Import raw ABI trace files
- ›Trim, predict and manually adjust peaks
- ›Bin peaks into alleles
- ›Tabular output of allele calls for downstream 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
Molecular Cloning
- ›Simulate restriction cloning, Gibson Assembly, Gateway cloning and TOPO cloning
- ›Automatically annotate plasmid maps and expression vectors
- ›Design primers and find CRISPR sites
- ›Optimize codons for your expression system
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
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
Workflows
- ›Visual editor for building automated bulk analysis pipelines
- ›20+ in-built workflows including Map Reads, Find SNPs and Apply Variants
- ›Create your own automated workflows to increase efficiency and reduce human error
- ›Connect directly to databases including UniProt, NCBI (Entrez), BLAST and PubMed
- ›Extend with custom code 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
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