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Biomatters Ltd
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
What's New
Version 7.1.4:
- Custom Blast: Fixed a bug with Custom Blast databases where the Accession numbers of hits wouldn't show up.
- Custom Blast: Fixed a bug with Custom Blast databases where certain original Geneious names for hit sequences wouldn't get returned.
- Custom blast: Reduced memory footprint of custom blast searches which had gone up in prior versions.
- Contig Viewer: Fixed hang viewing large circular contigs with consensus sequence numbering turned on.
- Contig Viewer: Fixed crash sometimes when reverting editing annotations.
- Consensus Alignment: Reduced memory usage and fixed crash when running low on memory.
- Read Mapping: Fixed crash when mapping large sequences or sequences with 100,000+ annotations to a reference sequence.
- Assembly: Fixed incorrect handling when a single input document contains a mixture of paired and unpaired reads.
- Fixed a bug where Geneious couldn't launch on Windows if the user's Path contained double-quotes.
- Annotations Table: Fixed crash when viewing multiple documents with lots of trim annotations.
- Backup: Fixed crash sometimes when backing up data.
- Realign regions / Concatenate alignments: Fixed crash sometimes when applying either of these to chromatograms.
- Workflows: Fixed 'Set Paired Reads' from workflows not respecting the selected options in some cases.
- Workflows: Fixed assembly so that all trimming options are avilable when running from a workflow.
- Workflows: Removed assembly 'sensitivity may be too high' warning that may show up each time you run a workflow.
- Group Sequences / Extract whole sequences: Now keeps custom properties added to the sequences.
Version 7.1.4:
- Custom Blast: Fixed a bug with Custom Blast databases where the Accession numbers of hits wouldn't show up.
- Custom Blast: Fixed a bug with Custom Blast databases where certain original Geneious names for hit sequences wouldn't get returned.
- Custom blast: Reduced memory footprint of custom blast searches which had gone up in prior versions. more...
Requirements
- Intel
- OS X 10.6 or later
- Java 6 or later
- 64-bit mode requires at least 4 GB of RAM
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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
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http://www.geneious.com/default,290,feature_comparison_chart.sm
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Pete028 reviewed on 10 Jul 2009
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mikenz reviewed on 22 Aug 2006
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,