What's New?

Geneious Prime 2021

Geneious Prime gets a new look

Enjoy the new look and feel of Geneious Prime with an updated design, including new icons and font.

New CRISPR on-target scoring method

Confidently design your guide RNAs using the Doench et al. 2016 CRISPR on-target scoring algorithm.

Accessible sequence viewer statistics

Easily sort and export your protein and nucleotide statistics within the document table.

Highlighted methylation sites for restriction enzymes

Quickly visualize restriction sites affected by Dam, Dcm and EcoKI methylation.

Many other small improvements
  • Easily shareable documents
  • Streamlined updating experience
  • Improved Vector NTI / GenBank imports
  • Added new genetic codes available on the NCBI list
  • And more….

Want more details?

All updates including minor changes and bug fixes can be viewed in the full Geneious Prime release notes

What Was Added in Previous Versions?

Geneious Prime 2020

Longread sequence mapping with Minimap2 (external plugin)
Fast and easy alignment of Oxford Nanopore and PacBio data to a reference sequence using an industry recommended tool, without the hassle of the command line
Clustal Omega replaces ClustalW for better, faster alignments
Scale up your alignments with Clustal Omega, now included with Geneious Prime. The HMM alignment engine improves both quality and speed of alignments compared to the older ClustalW aligner.
Better back translate and codon optimization
New codon optimization algorithm lets you match the codon usage from your organism of choice by generating a new sequence, starting from either a protein or nucleotide sequence. Optionally eliminate rare codons and restriction sites.
More accurate annotation of CDS features onto your plasmids
Automatic annotation of plasmids is now smarter with adjustment of CDS boundaries to match the nearest valid ORF when annotating single-interval CDSs from your reference features database.
Add your favorite tools to Geneious with improved Wrapper Plugin system
Can’t wait for us to add your favorite command line aligner, tree builder or assembler? You might be able to add it yourself from right inside Geneious using the Wrapper Plugin Creator plugin. Coding skills are not required, though a good understanding of command line interfaces and file formats is.
Long Read de novo Assembly with Flye (external plugin)
Fast de novo assembly of your raw Oxford Nanopore and PacBio long read sequences using Flye, suited to a wide range of applications including both single genome projects and metagenome assembly.
Import Metadata on to Sequences and other Documents
Seamlessly attach new data from downstream analyses or other applications onto your sequences in Geneious, or update document fields, by importing columns from a CSV/TSV format spreadsheet onto documents that are already in Geneious.
Annotate from Database Improvements
Easily identify and annotate the best matched features from a database on your plasmids and other sequences using the new extended database of standard plasmid features provided with Geneious, or use your own sequences as reference.
Codon Optimization and Back Translation Improvements
Customize the codon optimization parameters for your model organism by defining short sequence motifs to exclude from your optimized sequence, while easily generating multiple co-optimized versions of your sequence simultaneously.
Primer Specificity Testing
Be confident your primers will only bind in a single location with automatic identification of any additional, off target, binding sites found when using Test with Saved Primers. Off-target information for the tested document will be added to the new primer annotations.
Wrapper Plugin System Improvements
Customize Geneious with your own plugins using the wrapper plugin system, which now supports de novo assemblers, and running supported linux-only tools via the Windows Linux Subsystem.
Analyze CRISPR Editing Results
Easily align, cluster and visualize NGS reads from your CRISPR editing experiments. Analyze the frequency of variants and their protein effects from your application of choice, including HDR, NHEJ and base editors.
Enhanced Search Options
Quickly access your documents, folders, analysis tools and recently viewed items from a single unified interface.
Codon Optimization Improvements
Hover over your optimized codons for more information on synonymous codons and their frequencies.

Geneious Prime 2019

Rapid Manual Primer Design
Select desired binding site in the Sequence View to see real-time display of length and melting point (Tm) then easily add a primer annotation with a convenient new button.
Powerful Primer Annotation Display
5′ extensions (tails) on annotated primers are now displayed inside the sequence view to indicate the length of the extension, the nucleotides it contains and what functional elements are present such as restriction sites, spacers and tags.
Simplified Testing and Annotation of Existing Primers
Easily search all folders for primers that match a sequence of interest with the redesigned “Test with Saved Primers” operation. Copy and paste primers from other programs into the new “Add Primers” operation to find them on your target sequence in one step.
Drag and Drop Sequence Export
Export annotated sequences in GenBank format by simply dragging documents out of Geneious Prime and onto the desktop or into another program.
Easy Extraction of PCR and Restriction Digest Products
Shift click between two compatible primers or restriction enzymes for quick and easy extraction of their product from your sequence.
Improved Protein Statistics
Calculate on the fly statistics for protein sequences directly on nucleotide sequences within the Statistics panel
Improved GenBank Export
Export the information you need with your sequences using the simplified, flexible options to include your own Meta-Data fields and allow or constrain export parameters to suit downstream applications.
Publish Plugins via Internal Network
Create a curated list of plugins to offer privately to members of your organization via your internal network.
Customizable Text View – Sequence Layout 
Format to alter wrapping, numbering, sequence color and presence of reverse complement and translation
Customizable Text View – Alignment Layout
Format to alter numbering, sequence color and highlighting of agreements/disagreements to consensus
Customizable Text View – GenBank Format
GenBank format available for all individual sequences
Primer Specificity
Primer specificity automatically tested within the template sequence when designing primers, and presence of any additional binding sites recorded on the primer annotation
Primer Design Improvements
Option to control the minimum distance between primers designed on the same strand – defaults to minimizing creation of duplicate primers when multiple primer pairs are designed together
Annealed Oligo Cloning
Added workflow to create a sequence with annotated overhangs representing the sticky ends created by annealing two partially overlapping oligos
Sanger Sequencing Primer Design
Quickly design primers for Sanger sequencing of vectors, inserts or other sequences
Vector NTI Database Import
Easily import your complete Vector NTI database with simple drag and drop, for both Vector NTI Express and Advance databases.
Improved Text View Formatting of Sequences and Alignments
Support formatting and export of sequences in accordance with U.S. Patent Office requirements as well as other improvements.
Primer Characteristics
Quick and easy primer pairing in the Sequence View to link two primers of your choice and calculate pair dimer Tm and product size.
Easier Shared Database Rollout
Immediately access shared data and get straight to doing your research with a Geneious Shared database connections now able to be pre-configured by your IT team or admin when rolling out a version of Geneious Prime. Includes improved support for Windows authentication.

Geneious R11

Parrot
Volcano Plots for RNA-Seq Expression Analysis
Visualize gene expression in an interactive volcano plot that can be used to highlight and jump to differentially expressed genes.
Pretty PCA Plots
Create beautiful PCA plots with better labelling and new visualization options.
Silent Mutation Analysis for Restriction Sites
Automatically identify point mutations in a coding sequence that will introduce a restriction site without affecting the protein.
CRISPR Cpf1 Option
Added support for CRISPR-Cpf1 with a 5’ PAM site. Find sites in A and T rich sequences and with higher cleaving efficiency in vivo.
Create Enzyme Sets
What’s in the freezer? No longer pull information from other sources. Now you can easily create your own enzyme sets.
Better FASTQ Import
Paired reads can be associated with each other during import and Geneious will do it’s best to guess how they’re paired. Read technology can also be set.
Updated Mauve Plugin for Bacterial Genome Alignment
Now includes support for sequence lists and the MCM operation for reordering contigs, making it possible to align draft genomes and perform genome finishing.
CRISPR-Cpf1 Specificity Scoring
Confidently pick the best CRISPR-cpf1 guide RNA sites using a new specificity score which is calculated from an off-target analysis against your database of choice.
Smart NGS Import
Drop any assortment of SAM, BAM, GFF, BED, and VCF files into Geneious to import in one easy step, even if you have a mixture of different samples and reference sequences.
Better BLAST Server Management
Set up several BLAST server mirrors at once and choose the best one each time you do a search. No more switching mirrors each time.
NCBI BLAST Cloud Support
It’s never been easier to set up your own BLAST mirror thanks to NCBI BLAST Cloud. If you set up a mirror in this way, Geneious can now connect to it natively.
Concatenate by Index
Concatenate sequence lists and alignments by index, rather than by name, which is super useful for merging paired reads that don’t quite overlap.
CSV/TSV Export of Sequence Lists
Export all of the sequences in a sequence list along with their metadata to CSV or TSV so you can drop them in Excel or similar for further analysis.