Geneious Prime 2022.0 Feature Overview

Dark Mode
Comfortably analyze your data at any time of the day or night with Geneious Prime in dark mode (beta)

Apply Optimized Codon
Easily add and remove optimized codons to your sequence

Command Line Interface
Run Geneious Prime operations and workflows as part of your broader bioinformatic pipelines locally or execute on more powerful servers.
Learn how to run Geneious operations via the command line

Manage Document Table Columns
Quickly organize your data with multiple column selection

Highlight Mismatching Bases
Highlight mismatching base calls in your chromatograms

Experimental Features
Try out features we are experimenting with and let us know your thoughts

Geneious Prime 2021.0 Feature Overview

Geneious Prime 2021.1 Feature Overview

Geneious Prime 2021.2 Feature Overview

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.

Virtual gel improvements
Easily view multiple sequences with the display of restriction enzymes in lane headings, and quick access to an exportable list of fragments

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.

Adjustable sequence selection
Adjust either end of the selected region in the Sequence View by dragging.

Amino acid numbering
Live numbering can now be shown alongside the translated amino acids on nucleotide sequences.

New filter interface
Locate documents quickly in any table with the new filter button added to the status bar.

View CRISPR cut sites
Easily view and compare CRISPR cut sites between your guide RNAs

View invalid CDS annotations
Improve your cloning workflows by quickly determining CDS annotations with premature stop codons

Batch edit annotations
Quickly add or edit annotations in batch by copying properties from other annotations, sequences or documents

Long-read 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.

Custom Codon Usage Tables
Back translate and optimize codons using your own codon usage tables. Import standard formats from public databases or external codon analysis tools.

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, with new protein statistics added including charge at pH 7 and amino acid group counts.

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
GenBank format available for all individual sequences. Sequence layout format to alter wrapping, numbering, sequence color and presence of reverse complement and translation. Alignment layout to alter numbering, sequence color and highlighting of agreements/disagreements to consensus.

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. Quick and easy primer pairing in the Sequence View to link two primers of your choice and calculate pair dimer Tm and product size.

Vector NTI Database Import
Easily import your complete Vector NTI database with simple drag and drop, for both Vector NTI Express and Advance databases.

Restriction Enzymes
Methylation sensitivity information shown in tool tip when mousing over a restriction enzyme

Sanger Sequencing Primer Design
Quickly design primers for Sanger sequencing of vectors, inserts or other sequences

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.

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.