What's New in Geneious R11?

6 March 2018
The Geneious R11 update is here. R11.1 is free if you have a valid subscription or a perpetual version R11 license. If you are currently using a previous version-only licence (eg R10), you will have to purchase an upgrade.

Have an older version of Geneious? The Geneious that you know and love gets better every year. Upgrade now and you can enjoy R11 as well as all the features included in previous releases.

SnapGene File Import (R11.1)

Drop SnapGene *.dna sequence files into Geneious to seamlessly import sequences along with their annotations and other metadata.

CRISPR-Cpf1 Specificity Scoring (R11.1)

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 (R11.1)

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.

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.

RNA-Seq - Volcano Plot

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.

Silent Mutation Analysis for Restriction Sites

Automatically identify point mutations in a coding sequence that will introduce a restriction site without affecting the protein.

Pretty PCA Plots

Create beautiful PCA plots with better labelling and new visualization options.

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.

Better BLAST Server Management (R11.1)

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 (R11.1)

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 (R11.1)

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 (R11.1)

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.

New Features of Geneious R11

  • Analyze Silent Mutations – Annotate potential restriction sites that can be introduced by silent mutations
  • Volcano Plots – Visualize gene expression in an interactive view that synchronizes your selection with the Annotations and Sequence View
  • Better Fastq Import:
    • Paired reads can now be associated with each other during import and Genieous will do it’s best to guess how they’re paired
    • Read technology can also be set during import (read technology is used by some assemblers)
  • CRISPR Improvements:
    • Added support for Cpf1 enzyme variant with 5′ PAM site
    • Added ‘Target Sequence’ as a qualifier on CRISPR annotations
  • Cloning: Create an empty enzyme set via File > New and add enzymes to it
  • PCA Plots: Improved label positioning and added a legend
  • Sequence/Alignment View: Selections of multiple annotations are now synchronized with the Annotations view
  • Sequence/Alignment View: Added annotation filter ‘truncated’ term which matches annotations with a truncated interval
  • Workflows: Added ‘Group sequences by name’ workflow for grouping sequences with the same name prefix into a list
  • CSV/TSV Exporter: Now supports exporting in the compressed .csv.zip and .tsv.zip formats


  • Sequence View: When shift-clicking in circular sequences, the selection is now always made clockwise around the circular instead of selecting the shortest selection
  • Sequence View: In wrapped mode, improved performance and fixed transient rendering glitches when scrolling
  • Sequence/Alignment View: Stopped editing mode getting turned on automatically in some situations where it was unnecessary
  • Sequence/Alignment View: ‘Create separate annotation for each interval’ option now remembers whether it was previously on or not
  • Alignment View: Improved performance when zoomed out while showing translation
  • Alignment View: Improved performance when running ‘Live Annotate and Predict’ on alignments
  • Translation: Added ‘Remove final stop codon’ option to translation from sequence view
  • Backup: Now remembers the last backup location you used, separately from other export operations
  • NCBI Search: Added ‘Targeted Loci’ rRNA databases
  • Genbank Import: Correctly imports all sequences from gb files where some sequences end with a single CONTIG line
  • Genbank Text View: Shows Genbank entries in strict format
  • Sequence Extraction: When extracting using the annotations table without concatenating intervals, multi-interval annotations are now truncated (affects interval indices in result)
  • Expression Analysis: Added option to calculate expression levels for miRNA, ncRNA, or any annotation type that ends with RNA
  • Compare Expression Levels (Geneious method) and Calculate Expression Levels: Values produced now have 2dp instead of 1dp accuracy
  • Compare Expression Levels (DESeq2 method): Confidence and absolute confidence are now derived from adjusted p-values
  • Annotate from Database & Test with saved primers: Primer annotations that have identical binding site and extension are now merged
  • Primer Annotations: Primers with an extension are now visually different
  • Document Table: “Modified” date column is now displayed by default
  • Exporting Tables: Better default names when exporting Annotation or Restriction Fragment tables
  • Tadpole de novo assembly: If Tadpole produces no contigs, all messages produced by Tadpole are now included in message displayed in Geneious
  • Map to reference / de novo assembly: Algorithm names displayed in most locations are now shorter. e.g. replaced “Bowtie2 – Fast and accurate read mapper” with “Bowtie2”
  • De novo assembly: Added option to specify the minimum number of sequences a contig must contain before it may be circularized (previously this was always 3)
  • Security: Geneious now uses any CA trusted root certificates installed in the OS for SSL connections
  • Security: New Advanced Preferences option SSL.CustomTrustedCertificates allows storing one or more custom trusted CA root certificates for SSL connections
  • Cloning: Optimize Codons operation has move from the Annotate & Predict menu to the Cloning menu
  • Plugins: List of installed plugins is now sorted by description by default
  • Assembly: When assembling each list separately, if one set produces an error it no longer stops assembly of all other sets from running
  • Workflows: Added option to record the author of a workflow
  • Workflows: Added option to ‘Randomly Sample Sequences’ workflow to use the first N sequences from the source list (faster than randomly sampling)
  • GFF Exporter: Exports sequences in fasta-format at bottom of the file and does not export all-blank sequences

Plugin Development

  • Exposed option for choosing colors (Options.addColorChooserOption)
  • Added method for adding help button next to an option (Option.setHelp)
  • Added methods to access selected annotations from annotation generators via SequenceAnnotationGenerator.SelectionRange
  • Added method to access the Java binary used by Geneious at runtime (SystemUtilities.getJavaExecutable)

Geneious Server and Geneious Database Server:

  • Add support for installation on version 7.x of Red Hat Enterprise Linux (RHEL) and CentOS
  • Update to version 7 of Tomcat
  • Removed login option to accept untrusted certificates, superseded by SSL certificate related changes in Geneious
  • Add support for clusters that do not report status of jobs that have been completed, such as is the default for Univa

Want more details?

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