Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 28 (12), 1647-9

Geneious Basic: An Integrated and Extendable Desktop Software Platform for the Organization and Analysis of Sequence Data

Affiliations

Geneious Basic: An Integrated and Extendable Desktop Software Platform for the Organization and Analysis of Sequence Data

Matthew Kearse et al. Bioinformatics.

Abstract

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 http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

Figures

Fig. 1.
Fig. 1.
Modular overview of the Geneious Basic software stack. Top-most modules have dependencies on lower modules. The unshaded modules represent the publicly accessible modules for plugin development.
Fig. 2.
Fig. 2.
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.

Similar articles

See all similar articles

Cited by 3,238 articles

See all "Cited by" articles

References

    1. Altschul S.F., et al. Basic local alignment search tool. J. Mol. Biol. 1990;215:403–410. - PubMed
    1. Drummond, A.J. et al. (2010) Geneious v5.5. Available at http://www.geneious.com (last accessed 12 March 2012)
    1. Field D., et al. Open software for biologists: from famine to feast. Nat. Biotechnol. 2006;24:801–803. - PubMed
    1. Goecks J., et al. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11:R86. - PMC - PubMed
    1. Lu G., Moriyama E.N. Vector NTI, a balanced all-in-one sequence analysis suite. Brief. Bioinform. 2004;5:378–388. - PubMed
Feedback