Arlequin (version 3.0): an integrated software package for population genetics data analysis - PubMed (original) (raw)

Arlequin (version 3.0): an integrated software package for population genetics data analysis

Laurent Excoffier et al. Evol Bioinform Online. 2007.

Abstract

Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.

Keywords: AMOVA; Computer package; EM algorithm; gametic phase estimation; genetic data analysis; population genetics; spatial expansion.

PubMed Disclaimer

Similar articles

• Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.
  Excoffier L, Lischer HE. Excoffier L, et al. Mol Ecol Resour. 2010 May;10(3):564-7. doi: 10.1111/j.1755-0998.2010.02847.x. Epub 2010 Mar 1. Mol Ecol Resour. 2010. PMID: 21565059
• PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs.
  Lischer HE, Excoffier L. Lischer HE, et al. Bioinformatics. 2012 Jan 15;28(2):298-9. doi: 10.1093/bioinformatics/btr642. Epub 2011 Nov 21. Bioinformatics. 2012. PMID: 22110245
• fastsimcoal2: demographic inference under complex evolutionary scenarios.
  Excoffier L, Marchi N, Marques DA, Matthey-Doret R, Gouy A, Sousa VC. Excoffier L, et al. Bioinformatics. 2021 Dec 11;37(24):4882-4885. doi: 10.1093/bioinformatics/btab468. Bioinformatics. 2021. PMID: 34164653 Free PMC article.
• The HLA-net GENE[RATE] pipeline for effective HLA data analysis and its application to 145 population samples from Europe and neighbouring areas.
  Nunes JM, Buhler S, Roessli D, Sanchez-Mazas A; HLA-net 2013 collaboration. Nunes JM, et al. Tissue Antigens. 2014 May;83(5):307-23. doi: 10.1111/tan.12356. Tissue Antigens. 2014. PMID: 24738646 Review.

Cited by

• An integrative phylogeography for inferring cryptic speciation in the Alpheus lottini species complex, an important coral mutualist.
  Rouzé H, Knowlton N, Anker A, Hurt C, Wirshing HH, Van Wormhoudt A, Leray M. Rouzé H, et al. iScience. 2024 Sep 26;27(10):111034. doi: 10.1016/j.isci.2024.111034. eCollection 2024 Oct 18. iScience. 2024. PMID: 39474063 Free PMC article.
• Genetic Attributes and Conservation of an Endangered Giant Water Bug Species, Diplonychus esakii Miyamoto and Lee, 1966 (Hemiptera: Belostomatidae).
  Kim SY, Lim C, Kang JH, Bae YJ. Kim SY, et al. Insects. 2024 Sep 29;15(10):754. doi: 10.3390/insects15100754. Insects. 2024. PMID: 39452330 Free PMC article.
• Phylogeography and genetic structure of a Tertiary relict tree species, Tapiscia sinensis (Tapisciaceae): implications for conservation.
  Zhang J, Li Z, Fritsch PW, Tian H, Yang A, Yao X. Zhang J, et al. Ann Bot. 2015 Oct;116(5):727-37. doi: 10.1093/aob/mcv112. Epub 2015 Jul 17. Ann Bot. 2015. PMID: 26187222 Free PMC article.
• Endemic genotypes of Candida albicans causing fungemia are frequent in the hospital.
  Escribano P, Rodríguez-Créixems M, Sánchez-Carrillo C, Muñoz P, Bouza E, Guinea J. Escribano P, et al. J Clin Microbiol. 2013 Jul;51(7):2118-23. doi: 10.1128/JCM.00516-13. Epub 2013 Apr 24. J Clin Microbiol. 2013. PMID: 23616451 Free PMC article.
• Can soil seed banks serve as genetic memory? A study of three species with contrasting life history strategies.
  Mandák B, Zákravský P, Mahelka V, Plačková I. Mandák B, et al. PLoS One. 2012;7(11):e49471. doi: 10.1371/journal.pone.0049471. Epub 2012 Nov 21. PLoS One. 2012. PMID: 23185340 Free PMC article.

References

1. 1. Adkins RM. Comparison of the accuracy of methods of computational haplotype inference using a large empirical dataset. BMC Genet. 2004;5:22. - PMC - PubMed
2. 1. Belkhir K, Borsa P, Chikhi L, et al. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000. Université de Montpellier II; Montpellier: 2004. GENETIX 4.05, logiciel sous Windows pour la génétique des populations.
3. 1. Chakraborty R. Mitochondrial DNA polymorphism reveals hidden heterogeneity within some Asian populations. Am J Hum Genet. 1990;47:87–94. - PMC - PubMed
4. 1. Currat M, Ray N, Excoffier L. SPLATCHE: a program to simulate genetic diversity taking into account environmental heterogeneity. Mol Ecol. 2004;4:139–142.
5. 1. Excoffier L. Analysis of Population Subdivision. In: Balding D, Bishop M, Cannings C, editors. Handbook of Statistical Genetics. 2nd Edition. New York: John Wiley and Sons, Ltd; 2003. pp. 713–750.

LinkOut - more resources

• Full Text Sources

  • Europe PubMed Central
  • PubMed Central

• Other Literature Sources

  • The Lens - Patent Citations Database

• Miscellaneous

  • NCI CPTAC Assay Portal