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Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

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Kearse, Matthew, Moir, Richard, Wilson, Amy, Stones-Havas, Steven, Cheung, Matthew, Sturrock, Shane, Buxton, Simon, Cooper, Alex, Markowitz, Sidney, Duran, Chris, Thierer, Tobias, Ashton, Bruce, Meintjes, Peter, Drummond, Alexei·2012·Bioinformatics

DOI 10.1093/bioinformatics/bts199

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Abstract

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 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. Contact: peter@biomatters.com

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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669

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Hamilton, R., Gebbie, W., Bowman, C., Mantanona, A., & Kalyuzhnaya, M. G. (2025) · Applied and Environmental Microbiology · doi:10.1128/aem.01364-24 · Cited by 1

Authors: Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P., & Drummond, A.
Venue: Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2012-04-27
Volume: 28
Issue: 12
Pages: 1647-1649
ISSN: 1367-4803 (ISSN-L)
1367-4811
DOI: 10.1093/bioinformatics/bts199
OpenAlex: W2128880918
Cited by: 20,027
References: 1
FWCI: 92.47
Type: journal article
Language: en
Open access: hybrid

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

Abstract

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Integrity signals

Verification

Claims the paper makes

Self-check

Citations

Cites

Cited by

Metadata

Record

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