Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at, implemented in Java and supported on Linux, Apple OSX and MS Windows.
The software is also available from the Bio-Linux package repository at. 1 INTRODUCTION Research in the biosciences increasingly depends upon bioinformatics for the effective organization and analysis of biological data and experimental results. Having access to the appropriate bioinformatics tools is crucial to the success of any research project. The field of bioinformatics itself has previously been segregated into the parallel realms of data organization (databases, access, integration, web services and search tools) and data analysis (efficient algorithms and statistical modeling). As a result, a large proportion of bioinformatics work involves the chaperoning of data from a variety of sources through a pipeline of analysis tools. This approach typically involves a number of ad hoc labor-intensive steps to convert file formats and create transitional file types.
Geneious Basic was created to provide a general framework for research-focused bioinformatics tasks to overcome these challenges and take advantage of modern computing trends. Highlights of the platform include automated database searching, data backup functionality and an extensible API for the integration of novel bioinformatics analysis tools. 2 METHODS Geneious Basic is written in Java Swing to maximize interoperability among all commonly used operating systems.
Geneious 11.1. Geneious is a revolutionary bioinformatics software platform 11.1 Biomatters Ltd. Review Comments Questions & Answers Update program info. Geneious for Windows. Old versions. Geneious 9.1 Geneious 7.0 Geneious 5.6.
It is compiled under and requires Java 5 to run. The application provides core modules to enable the visualization, manipulation and transfer of DNA sequences (linear, circular and short oligos such as primers and probes), amino acid sequences, pair-wise and multiple alignments, phylogenetic trees, 3D structures, sequence chromatograms, contig assemblies, microsatellite electropherograms and statistical graphs. The underlying software framework for Geneious Basic is modular and multi-tiered with a focus on handling bioinformatics data and tools.
It integrates a comprehensive plugin system which is grounded in the extensible Geneious API. The public API component allows plugin developers to leverage the functionality and user interface of the Geneious platform while concentrating on the development of processes and algorithms. The API download from the Geneious website provides a number of skeleton plugin examples to use as a basis for new plugins, allowing developers with a basic level of Java knowledge to develop fully functional plugins that greatly extend the functionality of Geneious Basic. 3 RESULTS The Geneious Basic graphical user interface comprises of three main panels, a variety of pull-down menus and many right-click functions for common bioinformatics analyses. Geneious Basic displays selected file(s) in a variety of different ways including sequence view (linear and circular), dotplot view, query-centric alignment view, protein domain view, 3D structure view, text view and notes. A number of analysis algorithms are implemented within Geneious Basic.
For a given document, the user can select from among the appropriate analysis tools to process the data; for example, in the case of a sequence document, the user may choose to perform a BLAST search for a given query sequence against a specific online repository, align against other sequences or generate protein translations. The combinations of available tools and document types allow for the implementation of complex workflows in a single, consistent environment. The phylogenetic tree showing the relationship of a MT-CO1 sequence from an unknown source with similar public sequence. Sequences were identified from Genbank using BLAST. Sequences were downloaded then aligned using the Geneious Aligner and a phylogenetic tree built using PhyML. All of these steps were performed within Geneious Basic. Geneious Basic has an active community of plugin developers, using the public API to contribute third-party plugins and additional functionality within Geneious.
The Species Delimitation Plugin, a plugin for summarizing measures of phylogenetic support for user-selected collections of taxa on user-supplied trees , is one example of scientific research leveraging the Geneious public API for publishable academic research. At the time of the writing of this manuscript, there were nine available plugins for Geneious Basic , from plugins wrapping industry standard tools such as Phobos Tandem Repeat Finder (Mayer 2006–2010) to tools that exploit online compute resources such as Green Button. 4 DISCUSSION The functionality in Geneious Basic can be compared with a number of other desktop software packages, such as VectorNTI , CLC Bio, Sequencher (GeneCodes), Lasergene (DNAstar) and MEGA4. In comparison to the above, the focus of Geneious Basic is to provide an extensible desktop platform in which existing components can be leveraged by third-party plugin developers. This is a unique and important contribution to bioinformatics, allowing users to customize and extend core to their needs without significant manual intervention, matching the success of extensible platforms in parallel spaces such as network analysis and workflow management (; ). Also comparable is Geneious Pro , a commercial extension to Geneious Basic.
It shares the base functionality of Geneious Basic and additionally provides tools focused on data sharing, collaboration and advanced next-generation sequencing functionality. Geneious Basic brings together a large and disparate number of complementary data sources, analysis methods and visualization tools. It is the intention of the authors that by encouraging development to the public API new analysis methods and visualization tools will continue to grow and diversify the range of bioinformatics tasks available to all researchers. Geneious Basic is cross-platform and is available for Linux, Apple OSX and MS Windows as a standalone download. It is also available as a preconfigured package in the comprehensive Bio-Linux operating system.
Conflict of Interest: MK is currently employed by Biomatters Ltd, the makers of Geneious and hold share options as part of the company share options scheme. Altschul S.F., et al. Basic local alignment search tool. 1990; 215:403–410. Drummond, A.J.
(2010) Geneious v5.5. Available at (last accessed 12 March 2012). Field D., et al.
Open software for biologists: from famine to feast. 2006; 24:801–803. Goecks J., et al. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. 2010; 11:R86. Lu G., Moriyama E.N.
Vector NTI, a balanced all-in-one sequence analysis suite. 2004; 5:378–388. Masters B.C., et al. Species Delimitation - a Geneious plugin for the exploration of species boundaries.
2011; 11:154–157. Mayer,C. (2006–2010) Phobos 3.3.11. Available at (last accessed 12 March 2012). Schatz M.C., et al.
Cloud computing and the DNA data race. 2010; 28:691–693. Smoot M.E., et al. Cytoscape 2.8: new features for data integration and network visualization. 2010; 27:431–432. Tamura K., et al.
The Biology Network Bioinformatics news for genome hackers Information. If you have a specific bioinformatics related question, there is also the question and answer site and the next generation sequencing community. If you want to read more about genetics or personalized medicine, please visit. Information about curated, biological-relevant databases can be found in.
Multicore, cluster, and cloud computing news, articles and tools can be found over at. Getting a job in bioinformatics. Friends.
Hi guys, MD student here. I'm currently playing with Geneious prime, which is intended to be a magic Swiss knife in lab, permitting to do all the common things (reads assembly, clustering, phylogeny, etc.).
I've seen this software used in a paper by Zheng, from MIT (not exactly the worst place), and in many other high-cited researches. This software certainly uses already known tools, under a plug-in mask (BBtools, for example) using mainly a good GUI, with a very high price. Now, here's the question: how is really convenient actually for a lab to invest money on recruiting a bioinformatician instead of license for this pre-cooked softwares? I've played with Geneious a bit using the trial version. It works quite well (and it seems to be ultra easy to bypass the license check, lol). I’m a PhD student working in computational biology/virology.
I stick to mostly command line tools for my large scale bioinformatics analyses. But for smaller tasks, Geneious is great. I taught my undergrad how to use that. It helps that my institution has a floating license so it’s free for us to use. However to echo the others, just like having a set of pipettes doesn’t make someone a molecular biologist, having a Geneious license doesn’t replace a bioinformatician.
It’s a great first step but you need to learn how these tools work to truly do robust analysis. I consider Geneious to be invaluable; I use it every day.
The visualizations are great and it has enough tools for me to do some digging into the sample; I can quickly align two sequences and inspect the result or map some reads, use and export to almost all formats, really make I'm not about to waste thousands of dollars synthesizing parts that were constructed in a janky, poorly versioned and undocumented Jupyter notebook, etc. But with the power of open source tools and glorious AWS, I can probably download, QC, align/filter reads, de novo, annotate the contigs using either entire databases or a custom database of particular interest, and finish my morning espresso shots and the post-coffee smoke break before you've downloaded the data from the browser and loaded them in Geneious and finished preprocessing your reads. With Geneious you pay a hefty price for the convenience and aesthetics, and the costs rise exponentially as you increase in size or complexity. It's a good Swiss army knife, but sometimes you need power tools.