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

By T. Antao, Ana Lopes, R. Lopes, A. Beja-Pereira, Gordon Luikart. BMC Bioinformatics, 2008

1,152 citations recorded by the source corpus.

BackgroundTesting for selection is becoming one of the most important steps in the analysis of multilocus population genetics data sets. Existing applications are difficult to use, leaving many non-trivial, error-prone tasks to the user.ResultsHere we present LOSITAN, a selection detection workbench based on a well evaluated Fst-outlier detection method. LOSITAN greatly facilitates correct approximation of model parameters (e.g., genome-wide average, neutral Fst), provides data import and export functions, iterative contour smoothing and generation of graphics in a easy to use graphical user interface. LOSITAN is able to use modern multi-core processor architectures by locally parallelizing fdist, reducing computation time by half in current dual core machines and with almost linear performance gains in machines with more cores.ConclusionLOSITAN makes selection detection feasible to a much wider range of users, even for large population genomic datasets, by both providing an easy to use interface and essential functionality to complete the whole selection detection process.

Subfields: Epidemiology, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/691cd87771e12ce85d0308fc93a373c5843a5ec1

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Citations in the corpus

Experimental harvesting of fish populations drives genetically based shifts in body size and maturation (2013, methodology): “The FDist method (Beaumont and Nichols 1996), as implemented in the software LOSITAN – Selection Workbench (Antao et al. 2008), was used to estimate outlier loci from the entire dataset of 25 markers (microsatellites and candidate loci) in the F5 and F6 generations, using 50 000 simulations, an infi”
Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis (2012, methodology): “Th e second PC, which separates the cultivated varieties, contained the most overlap with the LOSITAN (Antao et al., 2008) outlier detection for SNPs on chromosome 4.”
Fine-scale spatial and temporal genetic structure of Atlantic cod off the Atlantic coast of the USA (2010, methodology): “Can J Fish Aquat Sci 65:1475–1486 Antao T, Lopes A, Lopes RJ, Beja-Pereira A, Luikart G (2008) LOSITAN: a workbench to detect molecular adaptation based on an Fst-outlier method.”