Geneious

Geneious combines all the major DNA and protein sequence analysis tools into one application.

• Sequence alignment
• Contig assembly
• Primers
• Cloning
• Restriction analysis
• BLAST
• Phylogenetics
• Automatic publication updates

The quoted price is that for a perpetual version-only license for non-commercial use. The pricing schema can be found here.

Note: Version 10 is a paid upgrade. Upgrade requests can be submitted here.

New

• Compare Expression Levels: PCA plots for multi-sample RNA-seq data
• Workflows: Added support for cloning operations

Bugs Fixes and Minor Changes

• Save as SVG Image: Added option to draw text as images so that the saved image more accurately matches what Geneious displays
• Save as PDF Image: Saved PDFs now use the same font as displayed in Geneious
• Tree Building: Fixed crash with third-party tree builders that don't provide any user-defined options
• BLAST from workflows: Fixed bug where it would use the default database instead of the selected database when run on a nucleotide sequence list
• Alignment Extraction: Fixed out-of-frame inline translation on alignments extracted from alignments when the extraction starts with an internal gap
• Workflows: Fixed bug where adding a new step would sometimes add it to the end of the workflow instead of after the currently selected step
• Sequence Editing: When deleting nucleotides from the start of a CDS annotation, the codon_start property is automatically adjusted to keep the translation of the remaining section of the annotation the same as it was previously
• Alignment/Contig View: Annotation tooltip 'Length' field has been renamed to 'Length (with gaps)' and a new 'Length' field introduced which contains the ungapped length
• Save as Image: Fixed sequence numbering getting slightly clipped sometimes on the right hand side of the image
• Restriction Cloning: Fixed bug where Workflows always used Enzyme Set instead of Annotated Enzymes, or where it couldn't be selected if the initial document didn't have annotated enzymes
• Restriction Cloning: Fixed poor performance when digesting large sequences into fragments
• Document Searching: Track names and properties on newly created or edited sequences are now indexed for searching in local and shared databases
• Document Searching: Improved speed for searches on large shared database
• Nexus Tree Importer: Internal node attributes can now be specified as branch support values or node labels and will behave appropriately when rerooting
• CSV Exporter: Better handling of descriptions that contain elements that look similar to html < tags /> but aren't
• De novo assembly: Fixed crash when using Windows 10 Insider Preview
• De novo assembly: Fixed crash in rare situations when the 'circularize contigs' and 'produce scaffolds' settings are both on (they are both on by default)
• Start up: Fixed crash on startup in rare situations on Windows
• NCBI Search: Fixed cases where summary documents were shown multiple times if connection was interrupted while the search was running
• Find Variants/SNPs: Fixed crash when setting strand-bias threshold to 50% when reads contain ambiguities
• NCBI Download: Fixed bug where genome summaries were not replaced by the full downloaded document if the summaries don't have a version number
• Printing/Saving As Image: Fixed bug where saving an image of an entire circular sequence while zoomed in would omit annotations outside the viewed region
• Find Heterozygotes: Fixed bug where no heterozygotes were found if only the left-hand end of the sequence was annotated as trimmed
• Genbank Document Exporter: When exporting strict Genbank format, annotation names are now saved as 'standard_name' qualifiers
• BBTools: Upgraded to version 37.25
• Sequence Extraction: When extracting a primer or probe from a sequence list the resulting document is now of type Oligonucleotide
• Optimize Codon Usage: Fixed bug running from Workflows where result sequence was identical to input
• Workflows: Added buttons to allow reordering of workflow steps
• Workflows: When run on operations that generate annotations on a referenced sequence in an alignment/contig (e.g., Find Variants/SNPs) added an advanced option for whether to propagate the annotations back to the referenced sequence
• Workflows: Replaced 'Truncate Annotations' workflow with 'Modify Annotation Intervals' workflow that also allows extending or shrinking annotation intervals
• Workflows: When an operation in a workflow saves documents to a sub-folder, those documents are now passed on to the next step in the workflow
• Sequence View: On multiple unaligned sequences, the little previous and next buttons for each annotation type now work
• Sequence View: Added "Don't show again" option to the message about there being too many annotation or track types to show them all in the controls
• Annotations Table: Order of columns can now be set under "Manage Columns"
• Document Table: Order of columns can now be set under "Manage Columns"
• Folders: Added "Collapse All" and "Expand All" options to right-click menu on folders that have subfolders
• Folders: Geneious now uses an icon to indicate if a folder is shared with other users, includes folders in a Shared Database or Geneious Server Database
• Shared Database: Folders created under the root folder will now always be created in a user's primary group
• Shared Database: Folders that are not created under the root folder will now always inherit the group of their parent folder
• Shared Database: Fixed a problem that prevented editing of group roles when using Oracle databases
• BBTools: Upgraded to version 37.17
• Map to reference: Improved alignment around gaps near ambiguity characters
• Map to reference: Fixed crash using "Assemble each list separately" when one of the lists contains no sequences
• Map to reference: Fixed bug where deletions of repeat regions over 15bp were not being discovered
• Map to reference: Fixed out of memory error when mapping reads (that should fail to map due to exceeding the maximum number of mismatches allowed) spanning the origin of a circular reference sequence
• Assembly / Map to reference: output contigs and consensus sequences record the algorithm used in the document description
• SPAdes assembler: Fixed so that if you are using an unsupported version of Windows, you can still run SPAdes on Geneious Server
• SPAdes assembler: The trusted and untrusted contigs options no longer default to the same trusted/untrusted contigs as you used for the previous assembly
• Contig View: Added option to sort reads by the number of differences from the reference sequence on contigs with fewer than 10,000 reads
• Sequence Extraction: Fixed crash extracting a region while also viewing an empty sequence
• Sequence Extraction and Merging Paired Reads: The 'Read Technology' field (and other fields) are copied to the derived documents
• Sequence Extraction and Translation: Fixed bug where translations were wrong after extracting a partial annotation on a circular sequence
• Copy Translation: Fixed crash copying from a circular sequence when the first codon spans the origin
• Alignment: Fixed crash sometimes when aligning after reverse complementing a sequence containing a mixture of DNA and RNA
• Alignment: Fixed crash when running MUSCLE on Windows when running from a data directory containing certain non-Latin characters (e.g., Chinese)
• Alignment: Fixed crash when running MAFFT on sequences containing inosine with "Automatically determine sequences' direction" turned on
• Gibson Assembly: If sequences are compatible it doesn't create primers and doesn't warn about filled in overhangs
• Gibson Assembly: RNA sequences used to create an invalid warning in the report about the reverse primer binding at multiple locations
• Cloning: Fixed crash when existing overhang annotations were adjacent to a cut site or PCR
• Cloning: Display warnings if similarity of overhangs is above threshold
• Gateway Cloning now records the used intervals and shows them in the lineage
• Lineage: Fixed incorrect interval when extracting a region across the origin from a circular sequence while viewing multiple sequences
• Primer Annotations: Fixed crash when trying to create a primer from an annotation that is between two bases
• Compare Expression Levels: Fixed crash that would occur when DESeq2 received a count table containing at lease one zero per gene
• Compare expression levels: Fixed crash when using Geneious method on multiple reference sequences when the first reference sequence does not contain both tracks
• SAM/BAM Export: Improved performance on data with high coverage paired reads (2 to 3 times faster)
• Tree Building: Fixed crash that could occur when building trees out of alignments backed by Genbank documents in some tree builders
• Tree Building: Fixed crash that could occur when cancelling a tree building operation on unaligned sequences
• Tree Viewer: Fixed missing attributes from "Show branch labels"
• 3D Structure viewer: Fixed background CPU usage sometimes after closing a view that was using the 'Spin' effect
• Data Location: Fixed crash after moving your Geneious data to a location that Geneious is unable to properly access (e.g. due to free low disk space)
• Repeat Finder: Fixed crash when finding repeats in the selected region only when the selected region spans the origin of a circular sequence
• Apply Variants to Reference Sequence: Fixed crash when running it on a sequence without variant tracks
• Find Variations/SNPs: Fixed incorrect protein effect for some start codon variants that would translate as M in a start codon but would translate differently at other positions (e.g. CTG translates as M as a start codon, but L elsewhere)
• Find Variations/SNPs: 'Protein Effect' field now says 'Start Codon Loss' if the start codon translation changes from M to a different amino acid
• Wrapper Plugins (e.g. RAxML, FastTree, Garli): When saving terminal output that is too long, the text will be truncated such that the first and last 500 lines are always retained
• Newick Tree Export: Fixed bug where exporting MrBayes trees with support values failed to save support values
• Document Notes: When text is too long to display in the "Info" tab, the text will be truncated such that the last 1000 characters are still shown
• Printing: Fixed hang that could happen when printing documents as images or PDFs
• General: Fixed crash sometimes when double clicking menu items
• General: Gracefully fail instead of crashing when Geneious data is in a Jottacloud synced folder which creates conflicting synchronization files

Geneious Server

• Fixed a bug where the new database administrator settings introduced in 10.2 were not initialized correctly and displayed the wrong values for new databases
• Fixed a bug where multiple dialogs would be displayed when user was disconnected
• Fixed various other bugs related to new settings introduced in 10.2
• Automatic creation of a private folder group for each user
• New database administrator settings. These are enabled for new databases, disabled for existing ones and can be changed at any time:
• Assign new folders under the root folder to the user's private group instead of the user's primary group
• Allow regular i.e. non-admin users to create and change the group of folders themselves
• Prevent users from storing new documents in the root folder
• "Show Inaccessible Folders" option is no longer available for Geneious Server Database
• Logging of events that affect user access to documents

Plugin Development

• Added new method, DatabaseService.showAdvancedSearchByDefault, to allow a database to show advanced search by defaults instead of basic
• Added new Options.addChildOptions() method that allows child options to stretch vertically
• Public API: Parameter names are no longer obfuscated