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

被引:957
作者
Antao, Tiago [1 ]
Lopes, Ana [2 ]
Lopes, Ricardo J. [3 ]
Beja-Pereira, Albano [3 ]
Luikart, Gordon [3 ,4 ]
机构
[1] Univ Liverpool, Liverpool Sch Trop Med, Liverpool L3 5QA, Merseyside, England
[2] Univ Porto, Fac Ciencias, Dept Quim, REQUIMTE, P-4169007 Oporto, Portugal
[3] Univ Porto, Ctr Invest Biodiversidad & Recursos Geneticos, P-4169007 Oporto, Portugal
[4] Univ Montana, Div Biol Sci, Missoula, MT 59812 USA
基金
比尔及梅琳达.盖茨基金会;
关键词
D O I
10.1186/1471-2105-9-323
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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 F(st)-outlier detection method. LOSITAN greatly facilitates correct approximation of model parameters ( e. g., genome-wide average, neutral F(st)), 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.
引用
收藏
页数:5
相关论文
共 12 条
[1]   Adaptation and speciation:: what can Fst tell us? [J].
Beaumont, MA .
TRENDS IN ECOLOGY & EVOLUTION, 2005, 20 (08) :435-440
[2]   Evaluating loci for use in the genetic analysis of population structure [J].
Beaumont, MA ;
Nichols, RA .
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 1996, 263 (1377) :1619-1626
[3]   POPULATION STRUCTURE AND HUMAN EVOLUTION [J].
CAVALLIS.LL .
PROCEEDINGS OF THE ROYAL SOCIETY SERIES B-BIOLOGICAL SCIENCES, 1966, 164 (995) :362-&
[4]   Computer programs for population genetics data analysis: a survival guide [J].
Excoffier, Laurent ;
Heckel, Gerald .
NATURE REVIEWS GENETICS, 2006, 7 (10) :745-758
[5]   Bioinformatics software for biologists in the genomics era [J].
Kumar, Sudhir ;
Dudley, Joel .
BIOINFORMATICS, 2007, 23 (14) :1713-1717
[6]  
LEWONTIN RC, 1975, GENETICS, V80, P397
[7]   The power and promise of population genomics: From genotyping to genome typing [J].
Luikart, G ;
England, PR ;
Tallmon, D ;
Jordan, S ;
Taberlet, P .
NATURE REVIEWS GENETICS, 2003, 4 (12) :981-994
[8]   Molecular signatures of natural selection [J].
Nielsen, R .
ANNUAL REVIEW OF GENETICS, 2005, 39 :197-218
[9]  
*R DEV COR TEAM, 2007, R LANG ENV STATT COM
[10]   GENEPOP (VERSION-1.2) - POPULATION-GENETICS SOFTWARE FOR EXACT TESTS AND ECUMENICISM [J].
RAYMOND, M ;
ROUSSET, F .
JOURNAL OF HEREDITY, 1995, 86 (03) :248-249