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

By Laurent Excoffier, Guillaume Laval, S. Schneider. Evolutionary bioinformatics online, 2005

2,723 citations recorded by the source corpus.

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.

Subfields: Genetics

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Citations in the corpus

Mitochondrial Control Region and microsatellite analyses on harbour porpoise (Phocoena phocoena) unravel population differentiation in the Baltic Sea and adjacent waters (2010, methodology): “For both mtDNA and microsatellites, analyses of molecular variance (AMOVA) were performed with ARLEQUIN 3.11 (Excoffier et al. 2005), assigning genetic variation to three levels, i.e., (1) among regions, (2) among subregions within regions, and (3) within subregions.”
Evaluation of Genetic Diversity and Genome‐wide Linkage Disequilibrium among U.S. Wheat (Triticum aestivum L.) Germplasm Representing Different Market Classes (2007, neutral): “01 (Excoffi er et al., 2005).”
Multiple introductions and invasion pathways for the invasive ctenophore Mnemiopsis leidyi in Eurasia (2011, methodology): “1 (Excoffier et al. 2005).”
Association mapping of yield and its components in rice cultivars (2007, methodology): “The software Arlequin 3.0 (Excoffier et al. 2005) performs the AMOVA procedure using SSR and standard multi-locus frequency data.”
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows (2010, methodology): “We describe here an updated and enhanced version of the ARLEQUIN population genetics package ( Excofﬁer et al. 2005), including a graphical (W INARL35 ) and a command-line ( ARLECORE ) version running both under windows, as well as command-line 32-and 64-bit Linux ARLECORE versions.”
Diversity distribution and population structure of tea germplasms in China revealed by EST-SSR markers (2011, positive): “The software Arlequin 3.01 was used to evaluate the population differentiation based on analysis of molecular variance (AMOVA) method (Excoffier et al. 2005).”
Circumpolar dispersal by rafting in two subantarctic kelp-dwelling crustaceans (2010, methodology): “Limnol Oceanogr 6:467–482 Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data.”
Genetic diversity and landscape genetic structure of otter (Lutra lutra) populations in Europe (2010, methodology): “The distribution of observed pairwise haplotype substitutions (mismatch distribution) was computed with ARLEQUIN 3.1.1 (Excoffier et al. 2005; http://cmpg.unibe.ch/software/arlequin3/), and a population-expansion test was performed using the sum of square deviation (SSD) between the observed and…”
Genetic structure of the giant kelp Macrocystis pyrifera along the southeastern Pacific (2010, positive): “Estimates of haplotype (He) and nucleotide (π) diversity were calculated for each population and for the entire dataset using ARLEQUIN V. 3.1 (Excoffier et al. 2005).”
Beyond the beneficial effects of translocations as an effective tool for the genetic restoration of isolated populations (2009, positive): “Genetic diversity estimates were calculated using the programs ARLEQUIN (Excoffier et al. 2005) and FSTAT Table 1 Genetic diversity estimates (microsatellite and mtDNA control region) for prairie-chicken populations Population Sample size (micro/mtDNA) Microsatellite DNA (6 loci) mtDNA control…”
Parasite diversity, patterns of MHC II variation and olfactory based mate choice in diverging three-spined stickleback ecotypes (2011, positive): “(Excoffier et al. 2005) to partition variance.”
Habitat fragmentation reduces genetic diversity and connectivity among toad populations in the Brazilian Atlantic Coastal Forest (2009, methodology): “We used the program Arlequin v. 3.0 (Excoffier et al., 2005) to calculate three population indices of genetic diversity: number of haplotype, nucleotide diversity, and haplotype diversity.”
Contrasting phylogeographical patterns for springtails reflect different evolutionary histories between the Antarctic Peninsula and continental Antarctica (2009, positive): “arlequin version 3.11 (Excoffier et al., 2005) was used to explore the genetic characteristics of populations and to test for the presence of population structure for each species separately.”
Genetic discontinuity among regional populations of Lophelia pertusa in the North Atlantic Ocean (2011, neutral): “1 (Excoffier et al. 2005).”
Role of domestication in shaping Castanea sativa genetic variation in Europe (2008, neutral): “0 software (Excoffier et al. 2005).”
PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R (2014, background): “However, these tend to specialize on specific subsets of analyses (e.g., Vilella 2005; Rozas et al. 2001; Purcell et al. 2007; Jombart 2008; Paradis 2010) or cannot process whole-genome data (e.g., Rozas et al. 2003; Excoffier et al. 2005).”