title: Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
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.
  
  
  METHODS
  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.
authors.affiliation: Biomatters Ltd., 2/76 Anzac Avenue, Auckland, 1010, New Zealand.
authors.forename: Matthew
authors.initials: M
authors.lastname: Kearse
authors.forename: Richard
authors.initials: R
authors.lastname: Moir
authors.forename: Amy
authors.initials: A
authors.lastname: Wilson
authors.forename: Steven
authors.initials: S
authors.lastname: Stones-Havas
authors.forename: Matthew
authors.initials: M
authors.lastname: Cheung
authors.forename: Shane
authors.initials: S
authors.lastname: Sturrock
authors.forename: Simon
authors.initials: S
authors.lastname: Buxton
authors.forename: Alex
authors.initials: A
authors.lastname: Cooper
authors.forename: Sidney
authors.initials: S
authors.lastname: Markowitz
authors.forename: Chris
authors.initials: C
authors.lastname: Duran
authors.forename: Tobias
authors.initials: T
authors.lastname: Thierer
authors.forename: Bruce
authors.initials: B
authors.lastname: Ashton
authors.forename: Peter
authors.initials: P
authors.lastname: Meintjes
authors.forename: Alexei
authors.initials: A
authors.lastname: Drummond
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D011381:Programming Languages; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface