Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

By Laurent Excoffier, Heidi E. L. Lischer. Molecular Ecology Resources, 2010

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View Paper: https://www.semanticscholar.org/paper/b91a36398ebe174f4044eb88debb2c26a335fd33

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Citations in the corpus

The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns (2019, methodology): “This scenario was simulated 1,000 times, and pairwise ΦST for each iteration was calculated using a batch version of arlsumstat (Excoffier & Lischer, 2010).”
Molecular tracing of confiscated pangolin scales for conservation and illegal trade monitoring in Southeast Asia (2015, methodology): “Tests for genetic differentiation between the two confiscations were performed using the analysis of molecular variance (AMOVA) procedure in Arlequin 3.5 (Excoffier and Lischer, 2010).”
tcsBU: a tool to extend TCS network layout and visualization (2016, methodology): “Different methods were developed to overcome such problems (e.g. Bandelt et al., 1999; Excoffier and Lischer, 2010).”
Phylogeography of Quercus aquifolioides provides novel insights into the Neogene history of a major global hotspot of plant diversity in south‐west China (2017, methodology): “We performed a hierarchical analysis of genetic differentiation for both cpDNA and SSR markers using an analysis of molecular variance (AMOVA) with 1,000 permutations as implemented in Arlequin 3.5 (Excoffier & Lischer, 2010).”
Gene Pools and the Genetic Architecture of Domesticated Cowpea (2013, methodology): “Fang et al. (2007) used amplified fragment length polymorphism markers to examine 15 landrace accessions of diverse origin and 72 advanced breeding lines and improved cultivars from four West African and two U.”
Continental‐scale assessment of genetic diversity and population structure in quaking aspen (Populus tremuloides) (2013, methodology): “Assessments of Hardy–Weinberg equilibrium (HWE) for all loci in all sampling sites and genotypic disequilibrium for all pairs of loci in all sampling sites were carried out in Arlequin 3.5.1.3 (Excoffier & Lischer, 2010).”
Haplotype phasing: Existing methods and new developments (2011, methodology): “Many software implementations of the EM algorithm exist, including Arlequi”
Phylogeographic consequences of different introduction histories of invasive Australian Acacia species and Paraserianthes lophantha (Fabaceae) in South Africa (2011, methodology): “All computations were carried out in Arlequin version 3.5 (Excoffier & Lischer, 2010).”
Abundance and community structure of ammonia-oxidizing bacteria and archaea in a temperate forest ecosystem under ten-years elevated CO2 (2012, methodology): “The variance components and FST evaluation of AMOVA are based on a multi-allelic model (Excoffier and Lischer, 2010), which relies on estimates of relationships between alleles in the same populations”
Testing the effect of palaeodrainages versus habitat stability on genetic divergence in riverine systems: study of a Neotropical fish of the Brazilian coastal Atlantic Forest (2015, methodology): “Standard population genetic summaries were calculated for each population and palaeodrainages using DnaSP (Librado & Rozas, 2009) and Arlequin 3.5 (Excoffier & Lischer, 2010).”
Relative effects of road mortality and decreased connectivity on population genetic diversity (2011, methodology): “5.1.2 (Excoffier and Lischer, 2010), we calculated two common metrics of genetic diversity (H = mean expected heterozygosity and A = mean allelic richness) and one metric of divergence (FST) to assess the effects of factor combinations on patterns of genetic variation.”
HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing (2016, methodology): “Several well established tools for further mtDNA data analysis such as ARLEQUIN (21), PAUP* (22) or MRBAYES (23) exist, but can currently not deal with the provided export format of HaploGrep.”