LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method

LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method

28 July 2008 | Tiago Antao, Ana Lopes, Ricardo J Lopes, Albano Beja-Pereira and Gordon Luikart
**LOSITAN: A Workbench for Detecting Molecular Adaptation Based on an Fst-Outlier Method** **Authors:** Tiago Antao, Ana Lopes, Ricardo J Lopes, Albano Beja-Pereira, Gordon Luikart **Abstract:** This article introduces LOSITAN, a user-friendly workbench designed to detect molecular adaptation using an Fst-outlier method. The tool simplifies the process of selecting loci under selection by providing an intuitive graphical user interface, data import and export functions, iterative contour smoothing, and the ability to generate graphics. LOSITAN leverages modern multi-core processors to parallelize the computation of Fst, significantly reducing processing time. The software is built on the fdist program, which evaluates the relationship between Fst and expected heterozygosity (H_e) under an island model. LOSITAN addresses the challenges of using Fst-outlier methods, such as data format requirements and parameter tuning, making selection detection more accessible to a broader range of users, even for large population genomic datasets. **Key Features:** 1. **User-Friendly Interface:** Directly usable from the web. 2. **Data Import/Export:** Supports Genepop format and export to R or spreadsheet software. 3. **Graphics Generation:** Offers multiple formats (PNG, SVG, PDF) and customization options. 4. **Parameter Tuning:** Automates the estimation of mean neutral Fst by removing potential selected loci. 5. **Multiple CPU Cores:** Utilizes multi-core processors to enhance computational efficiency. 6. **Automatic Updates:** Transparently downloads the latest version of fdist. **Conclusion:** LOSITAN is designed to make selection detection more accessible and accurate, addressing common issues in Fst-outlier methods. It leverages multi-core computing to improve performance and provides robust functionality for both researchers and non-experts. Future developments will include additional F-outlier methods and simulation facilities.**LOSITAN: A Workbench for Detecting Molecular Adaptation Based on an Fst-Outlier Method** **Authors:** Tiago Antao, Ana Lopes, Ricardo J Lopes, Albano Beja-Pereira, Gordon Luikart **Abstract:** This article introduces LOSITAN, a user-friendly workbench designed to detect molecular adaptation using an Fst-outlier method. The tool simplifies the process of selecting loci under selection by providing an intuitive graphical user interface, data import and export functions, iterative contour smoothing, and the ability to generate graphics. LOSITAN leverages modern multi-core processors to parallelize the computation of Fst, significantly reducing processing time. The software is built on the fdist program, which evaluates the relationship between Fst and expected heterozygosity (H_e) under an island model. LOSITAN addresses the challenges of using Fst-outlier methods, such as data format requirements and parameter tuning, making selection detection more accessible to a broader range of users, even for large population genomic datasets. **Key Features:** 1. **User-Friendly Interface:** Directly usable from the web. 2. **Data Import/Export:** Supports Genepop format and export to R or spreadsheet software. 3. **Graphics Generation:** Offers multiple formats (PNG, SVG, PDF) and customization options. 4. **Parameter Tuning:** Automates the estimation of mean neutral Fst by removing potential selected loci. 5. **Multiple CPU Cores:** Utilizes multi-core processors to enhance computational efficiency. 6. **Automatic Updates:** Transparently downloads the latest version of fdist. **Conclusion:** LOSITAN is designed to make selection detection more accessible and accurate, addressing common issues in Fst-outlier methods. It leverages multi-core computing to improve performance and provides robust functionality for both researchers and non-experts. Future developments will include additional F-outlier methods and simulation facilities.
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