What's New in Geneious Prime 2019.1?

The Geneious Prime 2019.1 update is here. The 2019.1 update is free to download if you have a valid subscription plan or a perpetual Prime 2019 license.

Have an old perpetual license for Geneious? The software that you know and love gets better every year. Update your plan now and you can enjoy Geneious Prime 2019 as well as all the features included in previous releases.

Geneious Prime 2019

Customizable Text View (2019.1)

Set your preferred layout in Text View for easy copying of sequences and alignments with customizable format including wrapping, numbering, sequence color and translations, or view sequences in GenBank format.

Primer Design Improvements (2019.1)

Easy identification of off-target primer binding sites, with automatic specificity checking against the template sequence during primer design, and a new setting to find more diverse primers in a primer design run.

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.

Annealed Oligo Cloning (2019.1)

Workflow to create a sequence with annotated overhangs representing the sticky ends created by annealing two partially overlapping oligos.

Restriction Enzymes (2019.1)

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

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.

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.

Publish Plugins via Internal Network

Create a curated list of plugins to offer privately to members of your organization via your internal network.

Usability Tweaks to Increase Efficiency

Enjoy an improved table of primers, drag and drop backbone selection for cloning, easier workflow management, better defaults, a less cluttered Sequence View and many other little tweaks and improvements.

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 R11

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.

Geneious R10

Smarter Restriction Cloning
Completely redesigned to be much simpler and more powerful. Includes automatic identification of compatible cut sites, and digestion and ligation with drag and drop ordering of fragments.
Alignment Masking
Mask unreliable alignment sites for better tree building, without deleting data. Manage alignment masking patterns using annotation tracks and automatically mask sites according to user defined criteria.
Improved Plasmid Viewer
The new circular overview option helps you stay oriented by showing the bases of the sequence and the plasmid map alongside each other with synchronized editing, selection and scrolling.
Chimera Filtering
Filter chimeric reads by comparing to a reference database, which can be any sequence list or alignment. Choose between the bundled public domain UCHIME algorithm or the faster USEARCH implementation.
Lineage View for Parent/Descendants
Lineage View is now easier to access as a separate tab and details about your cloning operations are shown right next to the relationships.
Assembly and Mapping
Better structural variant mapping, a new workflow to build SNP trees by applying variants to a reference and better de novo assembly of Ion Torrent, 454, and PacBio CCS data.
Improved Cloning
Gibson and Golden Gate now has sequence view of fragments within the options. Gibson assembly can now saves primers for easy ordering
Annotate from Database
Annotate nucleotide sequences from a protein database by comparing translations of the nucleotide sequence in all six frames with the protein database sequences
Zip Import
Zip files containing multiple files and sub-folders can now be imported
Sequence Viewer
Added ‘Copy Translation’ to translate selected regions of a nucleotide sequence (in right-click menu)
SPAdes de novo assembler
For MacOS/Linux: 64 bit OS is required. For Windows, 64 bit Windows 10 (with recent updates installed) is required. You also need to install additional Windows features (Instructions)
Find CRISPR Sites
Major performance improvements were made to the off-target scoring algorithm
All CRISPR sites will now be scored against all potential off-target sites in every run
Scoring CRISPR sites against off-targets now takes a seed region into account. This is a 10 bp region adjacent to the PAM site that can tolerate a maximum of 2 mismatches and 0 indels
RNA-Seq Expression Analysis
Compare Expression Levels now has the option to use DESeq2 for pairwise analysis with replicate samples and will produce a principle component analysis (PCA) plot for quality control.
Cloning Workflows
Restriction Cloning, Gibson Assembly and Golden Gate can now be incorporated into Workflows. Automate your cloning procedures or perform high-throughput batch cloning.

Geneious R9

R8 - Fennec Fox
Golden Gate
Intelligent handling of preconfigured Golden Gate parts and automatic designing of primers for new parts.
RNA- Seq and Structural Variant Mapping
Map RNA-seq using existing annotated coding regions or discover novel intron and fusion genes during mapping. For DNA sequencing, you can now discover structural variants and annotate them, allowing for correct alignments of read-ends around deletions and structural rearrangements in heterozygous samples.
Big Trees
New search box for finding nodes and taxa, and automatic collapsing of sub-trees based on distances. Greatly improved performance when loading and rendering trees.
Cutting edge CRISPR
New scoring strategy for on-target activity. Options to control how many mismatches and indels are allowed when scoring against off-targets.
VCF Export
Easy exporting of single-sample variants.
Brand new and super-fast de novo assembler with a very low miss-assembly rate.
Primer Design
Improved the speed on larger sequences when a target region and product size range have been specified
Read filtering with built-in BBTools

  • Merge paired reads using BBMerge
  • Error correction and coverage level normalization using BBNorm
  • Duplicate read removal using BBDedupe
  • BBDuk plugin for additional trimming (provides adapter, paired read overlap, quality, minimum length, and entropy trimming)
Even better support for HiDPI displays on Windows and Linux. Most importantly, the sequence and alignment view is now scaled according to your display.
Alignment and contig viewing
redesigned “go to next” controls give more power in a more intuitive interface.
Sequence view
Updated to new modern font for high quality publications, cleaner plasmid maps and retina screens.
Gibson Cloning
now fully supports the full array of scarless methods including SLIC, SLiCE, CPEC, InFusion and GeneArt Seamless.
New workflow to run batch reference mapping of many data sets against many references, matching them up by name.
Sequences in the multiple alignment are now highlighted according to coloring in the tree.
Parents and descendants are now shown with more information about the steps that have been performed and an HTML report can be exported with the full lineage.
New Plugins