Geneious Prime
Geneious Prime
2020.1.2

5.0

Geneious Prime free download for Mac

Geneious Prime

2020.1.2
07 April 2020

Sequence analysis software for molecular biologists.

Overview

Geneious Prime 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 subscription version license good for 1-year for non-commercial use. The pricing schema can be found here.

What's new in Geneious Prime

Version 2020.1.2:
Features:
  • Import metadata onto sequences and other documents from columns in a CSV/TSV format spreadsheet
  • Improved automatic annotation of plasmids and other sequences
    • Option to only annotate the best matching feature of a type at each location. If this option is selected only the annotation with highest similarity will be found at each location based on a specified overlap length
    • New database of standard plasmid features for use with Annotate from Database, with extended feature set, better conformation to GenBank annotation types and colouring of annotations for colored reporters that match the reporter colour
    • Pairwise alignment between query and reference now included on annotations for each match found using Annotate from Database
    • Addition of a 'Reference Features' folder as the default Source for Annotate from Database, to which additional folders with custom features can be added alongside the provided features
  • Codon Optimization and Back Translation improvements
    • Avoid defined short sequence motifs (as for RE sites), using a modification of the dynamic programming algorithm described in Condon and Thachuck (2012)
    • Generate multiple optimized versions of a sequence simultaneously, co-optimising to increase the pairwise distance between them
    • Restriction enzymes to avoid in the optimized result can now be fine-tuned by selecting a subset of the chosen enzyme set
    • List of codon usage tables included with Geneious reduced to only show high expression tables
    • Option to choose between producing different sequences or reproduce results when operation is re-run (default is to produce a different sequence each time)
  • Automatic primer specificity testing when running Test with Saved Primers to identify any additional 'Off-target' binding sites primers found on the sequence. Off-target information for the tested document will be added to the new primer annotations.
Minor Features:
  • Restriction Cloning: Option to specify a subset of enzymes to use from the selected enzyme set
  • Batch Rename sequences based on the name of an annotation that is present on the sequence
Plugin Development:
  • Wrapper Plugin system now supports:
    • de novo assemblers
    • Running Linux programs under the Windows Linux Subsystem
  • Wrapper Plugins - UI improvements:
    • Can now add a checkbox in the options boxed section heading
    • Added 'fill horizontal space' setting for allowing more flexibility in the user options layout
    • Added ability to specify a command line option for checkboxes which are unchecked
    • Can now add user options that are split into different sections on the command line
  • Wrapper Plugin system - other improvements:
    • Map to reference includes stdout & stderr in the assembly report if the 'Save standard out' option is on
    • Added variable for number of CPUs on the machine it is being run on
    • Added option for attaching TSV/CSV metadata to sequences produced by the plugin
  • Documents generated by SequenceAnnotationGenerators are now assigned unique names when they're added to a local database folder
  • Fixed various sequence copying methods to include all displayable fields on the created copy
Fixes and Minor Changes:
  • Document Table: Now considers spaces when sorting documents
  • History View: Entries can now be selected for copy-paste
  • History View: Show the fields within each history entry in a fixed order instead of random order
  • Sequence Assembly: Assembly reports are now saved by default
  • Alignment View: Highlighting is now on by default for pairwise alignments
  • Batch Rename: Added a warning to the preview panel indicating that the action cannot be undone
  • Restriction Enzymes: Default enzyme sets included with Geneious now update automatically on first launch
  • Virtual Gel: Fixed crash when enzymes have unknown cut sites
  • Cloning UI: Fixed bug where the sequence was deselected when changing enzymes or making other changes in the construct layout view
  • Cloning UI: Fixed bug where annotations table would sometimes show up below the sequence preview in the cloning options
  • Codon Optimization: Fixed a bug where users could accidentally select the dividing line between custom and bundled codon usage tables
  • Workflows: 'Group Sequences By Name' workflow now works on protein sequences
  • Workflows: When a workflow exposes an option which is not applicable to the selected documents, Geneious now fails to run with an informative message instead of crashing
  • Workflows: Fixed crash on startup after external file synchronization software has created extra files in your database when detecting conflicts
  • Contig Assembly: When assembling by name, if all sequences within sequence lists have identical values for a particular field then that value is now copied to resulting contig assemblies
  • Map to Reference and de novo Assembly: CPU usage now excluded from assembly report for non-Geneious algorithms, as the value reported was incorrect
  • SPAdes Assembler: Fixed canceling under Windows to actually stop the SPAdes program
  • Export: Truncate long document names automatically instead of failing to export
  • Export: Improved export to Geneious format to fail gracefully rather than creating an invalid Geneious file when there is a problem loading documents referenced by the document being exported
  • Export: SAM/BAM export uses sample name instead of document name as read group sample name field
  • Import/Export: BED format now accommodates undirected annotations (previously undirected annotations were treated as forward directed annotations)
  • Import: Fixed SAM/BAM import failure when importing a large file which contain a read with a name over 255 characters long
  • Import: SAM/BAM import will now fail with an appropriate message instead of crashing when SAM/BAM file is corrupt
  • Sequence View: Display primer extensions that go beyond the end of the sequence
  • Sequence View: Fixed bug where repeat finder annotation links to other locations in the sequence didn't work if the sequence name contained a colon
  • Sequence View: Fixed the chromosome selector so that it doesn't truncate long sequence names when showing the drop down list
  • Sequence Extraction: Fixed a bug where "Extract Digestion Fragment" could crash for restriction sites located right at the origin
  • Test with Saved Primers: Increased size of number input fields on Linux and MacOS
  • Primer Characteristics: Fixed crash when trying to calculate characteristics for sequences with very high degeneracy
  • Primer Design: "Design for Sequencing" no longer incorrectly generates paired primers
  • Local Documents: Fixed occasional crash that could happen at any time during background indexing
  • General: Fixed crash which occurred sometimes after pasting undisplayable text into input dialogs
  • Sequencing Profiles: Fixed crash when drag’n’drop importing an exported profile
  • Linux UI: GTK version 3 is now used if available, on Linux distributions other than Ubuntu
  • Shared Database: Non-shared workflows are no longer stored in shared databases
  • Shared Database: Read-only folder status is now updated correctly when changed (previously required restart for some changes to show in UI)
  • Shared Database: The delete, rename, change folder color actions enabled state now accurately reflects folder permissions
  • Shared Database: Prevent adding new user accounts with duplicate names
  • Shared Database: Fixed bug whereby new user accounts were created in Geneious when the Username was typed with different capitalization or spaces at the front and end
  • Shared Database: Fixed poor performance connecting to a shared database which had hundreds of workflows
Other Notes:
  • An email address is now required for account management purposes and to make sure we can contact you with important updates
  • Java Version: Update bundled JRE to 11.0.6 for macOS

Join over 500,000 subscribers.

Subscribe for our newsletter with best Mac offers from MacUpdate.

5 Geneious Prime Reviews

Rate this app:

Mikenz
22 August 2006

Most helpful

For a long time scientists who generate or analyse DNA sequences have been using multiple pieces of software to: 1) view chromatographs, 2) trim sequences 3) Blast data 4) align sequences 5) build phylogenetic trees. Chopping and changing between different file formats and at times different operating systems (Mac, PC, Unix/Linux) has been a frustrating and time-consuming exercise. Current and future releases of Geneious (www.geneious.com) offer a solution to (most) of these frustrations. The software logo “research in a flash” accurately describe the potential of Geneious - only months after its release it has become the “Swiss army knife” of bioinformatics software. The user interface of Geneious is both attractive and intuitive. While the software has some “bell and whistles” for more complex tasks one of its key attributes is a simple user interface. Earlier this year I used the Beta-release in some undergraduate teaching labs - with great success. Students did a Genbank search, downloaded files, did an alignment and built a phylogenetic tree (with bootstrapping) all in the blink of an eye. If you are looking for a piece of bioinformatics software for teaching purposes look no further than Geneious. With the integration of sequence chromatograph viewing and editing of DNA sequences/alignments (new in version 2) Geneious is now firmly embedded in my research practices. As is the case with any new software there are a few features that don't work quite as well as you might like - but the good news is that if you write to them they will likely fix it up asap. My request to provide a variety of nucleotide colour schemes was implemented within 2 weeks. Moreover, the software is structured in such a way that “new” plugins can be written and incorporated with relative ease. The Geneious team has made available a freeware version and a pro version that (for a price) allows you to access more functionality. Based on the hours of time this program has saved me already I would not even blink at the academic price tag of $133 (USD) - or cheaper for students. The software almost has too many features to comment on in any one review (e.g. “agents” and collaboration modes) - the best advice I can give is to download it, do the tutorial and test drive it on a bioinformatics task that you regularly conduct - it won't disappoint. Cheers,
Like (4)
Version 2.0.4
Vitaly
23 April 2012
it's 5.6.2
Like
Version 5.6.1
Frankof
10 October 2011
"free" in this case means $795. Oh, well.
Like (1)
Version 5.5.3
3 answer(s)
Regular-Warren
Regular-Warren
10 October 2011
Thanks for pointing out the error in our listing. I've updated it (based on the "Student pricing option listed on the developer's site).
Like (1)
SickTeddyBear
SickTeddyBear
02 November 2011
The basic version is free for academic/student use. Here's a feature comprison: http://www.geneious.com/default,290,feature_comparison_chart.sm
Like
Frankof
Frankof
03 November 2011
@Negritude: thanks for the info. However, a sequence analysis program that in the free version does not even allow editing sequences (let alone sequence alignments and annotations), or the search for ORFs, or primer design, is hardly useful. I recommend "SerialCloner" which does a good job in my lab, and is really free.
Like (1)
SickTeddyBear
30 March 2011
Note that 5.4.0 is a beta. The current stable release is 5.3.6. Check the developer's web site for more info.
Like
Version 5.4.0
1 answer(s)
SickTeddyBear
SickTeddyBear
19 April 2011
5.4.1 is also beta.
Like
Pete028
10 July 2009
Geneious is a superb piece of software for all molecular biologists. I love it. It saved me heaps of time.
Like (1)
Version 4.7.1
Mikenz
22 August 2006
For a long time scientists who generate or analyse DNA sequences have been using multiple pieces of software to: 1) view chromatographs, 2) trim sequences 3) Blast data 4) align sequences 5) build phylogenetic trees. Chopping and changing between different file formats and at times different operating systems (Mac, PC, Unix/Linux) has been a frustrating and time-consuming exercise. Current and future releases of Geneious (www.geneious.com) offer a solution to (most) of these frustrations. The software logo “research in a flash” accurately describe the potential of Geneious - only months after its release it has become the “Swiss army knife” of bioinformatics software. The user interface of Geneious is both attractive and intuitive. While the software has some “bell and whistles” for more complex tasks one of its key attributes is a simple user interface. Earlier this year I used the Beta-release in some undergraduate teaching labs - with great success. Students did a Genbank search, downloaded files, did an alignment and built a phylogenetic tree (with bootstrapping) all in the blink of an eye. If you are looking for a piece of bioinformatics software for teaching purposes look no further than Geneious. With the integration of sequence chromatograph viewing and editing of DNA sequences/alignments (new in version 2) Geneious is now firmly embedded in my research practices. As is the case with any new software there are a few features that don't work quite as well as you might like - but the good news is that if you write to them they will likely fix it up asap. My request to provide a variety of nucleotide colour schemes was implemented within 2 weeks. Moreover, the software is structured in such a way that “new” plugins can be written and incorporated with relative ease. The Geneious team has made available a freeware version and a pro version that (for a price) allows you to access more functionality. Based on the hours of time this program has saved me already I would not even blink at the academic price tag of $133 (USD) - or cheaper for students. The software almost has too many features to comment on in any one review (e.g. “agents” and collaboration modes) - the best advice I can give is to download it, do the tutorial and test drive it on a bioinformatics task that you regularly conduct - it won't disappoint. Cheers,
Like (4)
Version 2.0.4