Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows - PubMed (original) (raw)
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
Laurent Excoffier et al. Mol Ecol Resour. 2010 May.
Abstract
We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute summary statistics (arlsumstat). The command-line versions run under both Linux and Windows. The main innovations of the new version include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans. Command-line versions are designed to handle large series of files, and arlsumstat can be used to generate summary statistics from simulated data sets within an Approximate Bayesian Computation framework.
© 2010 Blackwell Publishing Ltd.
Similar articles
- Arlequin (version 3.0): an integrated software package for population genetics data analysis.
Excoffier L, Laval G, Schneider S. Excoffier L, et al. Evol Bioinform Online. 2007 Feb 23;1:47-50. Evol Bioinform Online. 2007. PMID: 19325852 Free PMC article. - QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations.
Yang J, Hu C, Hu H, Yu R, Xia Z, Ye X, Zhu J. Yang J, et al. Bioinformatics. 2008 Mar 1;24(5):721-3. doi: 10.1093/bioinformatics/btm494. Epub 2008 Jan 17. Bioinformatics. 2008. PMID: 18202029 - TNT version 1.6, with a graphical interface for MacOS and Linux, including new routines in parallel.
Goloboff PA, Morales ME. Goloboff PA, et al. Cladistics. 2023 Apr;39(2):144-153. doi: 10.1111/cla.12524. Epub 2023 Jan 22. Cladistics. 2023. PMID: 36682054 - NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne ) from genetic data.
Do C, Waples RS, Peel D, Macbeth GM, Tillett BJ, Ovenden JR. Do C, et al. Mol Ecol Resour. 2014 Jan;14(1):209-14. doi: 10.1111/1755-0998.12157. Epub 2013 Aug 31. Mol Ecol Resour. 2014. PMID: 23992227 - Joint analysis of demography and selection in population genetics: where do we stand and where could we go?
Li J, Li H, Jakobsson M, Li S, Sjödin P, Lascoux M. Li J, et al. Mol Ecol. 2012 Jan;21(1):28-44. doi: 10.1111/j.1365-294X.2011.05308.x. Epub 2011 Oct 14. Mol Ecol. 2012. PMID: 21999307 Review.
Cited by
- Ficus insipida subsp. insipida (Moraceae) reveals the role of ecology in the phylogeography of widespread Neotropical rain forest tree species.
Honorio Coronado EN, Dexter KG, Poelchau MF, Hollingsworth PM, Phillips OL, Pennington RT, Carine M. Honorio Coronado EN, et al. J Biogeogr. 2014 Sep;41(9):1697-1709. doi: 10.1111/jbi.12326. J Biogeogr. 2014. PMID: 25821341 Free PMC article. - Geographical parthenogenesis and population genetic structure in the alpine species Ranunculus kuepferi (Ranunculaceae).
Cosendai AC, Wagner J, Ladinig U, Rosche C, Hörandl E. Cosendai AC, et al. Heredity (Edinb). 2013 Jun;110(6):560-9. doi: 10.1038/hdy.2013.1. Epub 2013 Feb 13. Heredity (Edinb). 2013. PMID: 23403961 Free PMC article. - Temporal migration rates affect the genetic structure of populations in the biennial Erysimum mediohispanicum with reproductive asynchrony.
Muñoz-Pajares AJ, Abdelaziz M, Picó FX. Muñoz-Pajares AJ, et al. AoB Plants. 2020 Jul 25;12(4):plaa037. doi: 10.1093/aobpla/plaa037. eCollection 2020 Aug. AoB Plants. 2020. PMID: 32904355 Free PMC article. - Comparative phylogeography of Mississippi embayment fishes.
Egge JJ, Hagbo TJ. Egge JJ, et al. PLoS One. 2015 Mar 31;10(3):e0116719. doi: 10.1371/journal.pone.0116719. eCollection 2015. PLoS One. 2015. PMID: 25826456 Free PMC article. - Variability and forensic efficiency of 12 X-STR markers in Namibian populations.
Calò L, Gentile F, Baio E, Raschellà C, Capelli C, Marino A. Calò L, et al. Int J Legal Med. 2024 Nov;138(6):2289-2298. doi: 10.1007/s00414-024-03299-9. Epub 2024 Aug 6. Int J Legal Med. 2024. PMID: 39105780 Free PMC article.
LinkOut - more resources
Full Text Sources
Molecular Biology Databases