Previous Geneious Versions

Here you can find a list of all the previous major releases of Geneious.

R10

R10_Full_Release
4 October 2016
10.0 release notes
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.
R10.1 Update
7 February 2017
R10.1 release notes
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
R10.2 Update
6 June 2017
R10.2 release notes
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.

R9

R9_Full_Release
7 October 2015
9.0 release notes
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.
Tadpole
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)
New Plugins

  • BBMap mapper for DNA/RNAseq
  • EupathDB for searching and retrieving eukaryotic pathogen sequences
  • Repeat Finder for annotating all regions that are repeated elsewhere in a sequence
R9 Update
1 March 2016
R9.1 release notes
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.
Assembly
New workflow to run batch reference mapping of many data sets against many references, matching them up by name.
Trees
Sequences in the multiple alignment are now highlighted according to coloring in the tree.
Lineage
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.

R8

R8_Full_Release
9 September 2014
8.0 release notes
16S Biodiversity Tool
A cloud-based tool that identifies high-throughput 16S rRNA amplicons from environmental samples using the RDP database, and visualizes biodiversity as interactive graphs and charts using a secure web viewer.
Sequence Classifier Plugin
Taxonomically classifies an organic sample by how similar its DNA is to your own database of known sequences using a BLAST-like algorithm with multiple loci and trees to assist with identification.
CRISPR Design
Locate potential CRISPR target sites using innovative heatmap-style annotations to assess sites based on off-target interaction.
Powerful NGS Assembly
Longer contigs, scaffolding and greater accuracy.
RNA-Seq Expression Analysis
Brand new functionality for transcriptomics!
Greater Workflow Configurability
New Genome finishing workflow and more options for creating custom workflows
Easier Plugin Development
Add your favourite algorithm, database or visualization to Geneious or write a plugin for your own new program and share it with the community
New Plugins
Extended functionality for tree building and viewing, alignment and assembly.

  • CRT – (by Chris Duran) Identifies existing known CRISPR sites in bacteria and archaea.
  • FLASH – (by Dave O’Connor)- Merge paired sequencing reads using FLASH
  • SeqPartitioner – (by Jed Barlow) – Partition allele multisets from multiple alignments
  • Augustus – (by Michael Thon) Predict genes using the Augustus algorithm.
  • EMBOSS Nucleotide Analysis – (previously bundled) Search for transcription factors, and predict protein coding regions.
  • EMBOSS Protein Analysis – (previously bundled) Predict secondary structure, antigenic regions and signal cleavage sites.
  • Go To Documents – Jump to documents by entering their unique IDs
  • Find Big Folders Workflow – List the size of all folders in your local database
  • Groovy Console – Opens a terminal window inside Geneious for scripting in the Groovy language.
R8 Update
3 March, 2015
8.1 release notes
Choicer chooser
Store commonly used sequences such as reference genomes, vectors and biological parts in separate folders from your working data, then easily choose them when you run Map to Reference or Gibson Assembly.
Sort by GC Content
All newly created nucleotide alignments, contigs, sequence lists, and sequences have a %GC field in the document table. Sequences in alignments, contigs and lists can be sorted by %GC.
Improved Primer Design for qPCR
Batch design primers for many regions within a single sequence in one step, great for qPCR design. Primer design and testing now have an option to match each sequence in an alignment (instead of just the consensus)
Extract more annotation information
Now you can select upstream, downstream and intergenic regions of matching annotations.
Mapping Qualities now included
Geneious mapper produces mapping qualities, SAM/BAM import/export handles mapping qualities, contig viewer displays mapping quality in status bar, added mapping quality color scheme
Integration with LIMS and external web-based systems
Geneious documents can now be opened by clicking a link in external web-based systems.
Easier Exporting for Newick and FASTA formats
Documents can now be exported in the compressed .fasta.gz and .fastq.gz formats. Export Tree documents: Export to newick format may now include bootstrap support values​
New Plugins

  • Blast2GO – All in one functional annotation tool and annotation data analysis.
  • FreeBayes – Haplotype-based variant detector for single sample analysis.

R7

R7_Full_Release
3 September 2013
7.0 release notes
Workflows
Easily create and share workflows based on your data and analysis. Try some of the built-in workflows or design your own.
Gibson Assembly
One-step cloning of fragments using Gibson assembly including automated primer design and batch cloning/shuffling
Codon Optimization
Find rare codons or produce a fully optimized sequence based on a target organism and remove unwanted restriction sites at the same time.
TOPO Cloning
One-step cloning of fragments into a vector using TOPO
Copy and Paste Annotations
Annotations are now maintained when copying sequences! Highlight part of a sequence, copy with ctrl+c and then paste it using ctrl+v into another location and the annotations will be preserved.
Better Coverage Analysis
Get more meaning from your alignments with added visualization of coverage.
New Plugins
Extended functionality for tree building and viewing, alignment and assembly.

  • RAxML – Randomized Axelerated Maximum Likelihood
  • GARLI – Genetic Algorithm for Rapid Likelihood Inference
  • FastTree – Approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences
  • LastZ – BLAST-like alignment tool for the pairwise alignment of chromosome-sized nucleotide sequences
  • Bowtie2 – Short read aligner
  • Velvet – De-novo assembler for very short reads
R7 Update
4 February 2014
7.1 release notes
Circular Assembly
Geneious can create circular contigs in its famous sequence viewer making it easier to assemble genomes such as bacterial genomes and plasmids.
Trio Analysis
The improved ‘compare annotation’ interface gives better results and more powerful options for SNP analysis and all results include annotation properties.
Strip Alignment columns
Build better trees! Remove columns with at least one ambiguity or strip two columns per codon.
Extract more annotation information
Now you can select upstream, downstream and intergenic regions of matching annotations.
New Plugins

  • TopHat – Fast splice junction mapper for RNA-Seq reads.
  • MIRA – Specialized assembler for sequences with a high number of repeats

R6

R6_Full_Release
4 October 2012
6.0 release notes
Latest Primer3 engine
Including brand new thermodynamic calculations that give you better stats on primers.
Automatic plasmid annotation
No more manual searching. New automatic plasmid annotation lets you sort through your data faster than ever before, saving your time and your eyesight.
Read Mapping
New fine-tuning algorithm quickly generates accurate results using less memory.
Enhanced Variant and SNP calling
Eliminate false variants, annotate average quality, find variations within specified annotations. dbDNP and db_xref annotations now hyperlinked.
Greater file format capability
More options for VCF, SWF, FASTQ, SAM/BAM and zipped files
New ‘info’ tab
View lineage, history and edit common fields in properties such as description and organism
R6 Update
7 February 2013
6.1 release notes
No more binding to known repeats
The Primer Design tools now include a repeat library mispriming function that prevents binding to known repeats, saving you time.
BLAST+
Custom BLAST now supports BLAST+ for increased search performance.
Enhanced DNA/RNA fold view
The DNA/RNA fold view is now available on two sequences, showing how the two molecules bind to each other (using Vienna rnacofold 2.0.7). We’ve also updated the stats panel, improved the probability color scheme, and implemented new energy models, giving you greater visibility than ever.