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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.
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
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 about phylogenetic tree building
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
- Import raw ABI trace files
- Trim, predict and manually adjust peaks
- Bin peaks into alleles
- Produce tabular output of allele calls
- Learn more about microsatellite analysis
Get started with Geneious today