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

BMC Bioinformatics. 2008 Jul 28;9:323. doi: 10.1186/1471-2105-9-323.

Abstract

Background: Testing 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.

Results: Here 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.

Conclusion: LOSITAN 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Computer Graphics
  • Computer Simulation*
  • Databases, Genetic
  • Evolution, Molecular
  • Genetics, Population / methods*
  • Genomics / methods
  • Selection, Genetic
  • Time Factors
  • User-Computer Interface