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Arlequin specifications


Unique identifier OMICS_11081
Name Arlequin
Software type Toolkit/Suite
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Laurent Excoffier

Publications for Arlequin

Arlequin citations


Widespread plant specialization in the polyphagous planthopper Hyalesthes obsoletus (Cixiidae), a major vector of stolbur phytoplasma: Evidence of cryptic speciation

PLoS One
PMCID: 5940214
PMID: 29738577
DOI: 10.1371/journal.pone.0196969

[…] Genetic variations within and among host-plant associations were estimated with pairwise F-statistics [] implemented in Arlequin v. []. Mitochondrial haplotype diversity was calculated for each of the 55 H. obsoletus populations (number and frequency of haplotypes). Standard molecular diversity indices (FST and […]


Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic

BMC Evol Biol
PMCID: 5930823
PMID: 29720079
DOI: 10.1186/s12862-018-1179-0

[…] ng coefficient (Fis), and tested for Hardy-Weinberg Equilibrium (HWE) using FSTAT []. We also assessed mitochondrial diversity by computing haplotype diversity (Hd) and nucleotide diversity (п) using Arlequin []. Given their admixed genetic nature, we did not perform such analyses for the continental populations. […]


Polymorphism in merozoite surface protein 7E of Plasmodium vivax in Thailand: Natural selection related to protein secondary structure

PLoS One
PMCID: 5931635
PMID: 29718980
DOI: 10.1371/journal.pone.0196765

[…] ]. The fixation index (Fst) was deployed to evaluate the level of population differentiation due to genetic structure by using different hierarchical analyses of molecular variance implemented in the Arlequin software version 3.11 []. Significance levels of the fixation indices were determined by permutation test. Phylogenetic trees were constructed using the maximum likelihood method based on the […]


Genetic polymorphisms in very important pharmacogenomic variants in the Zhuang ethnic group of Southwestern China

PMCID: 5944516
PMID: 29703042
DOI: 10.1097/MD.0000000000010559

[…] To analyze the pairwise genetic distance among populations, pairwise Fst values were calculated using Arlequin v3.5. Population structure was investigated using the Bayesian clustering algorithm STRUCTURE ver. 2.3.1 (Pritchard Lab, Stanford University, […]


Genetic structure of South African Nguni (Zulu) sheep populations reveals admixture with exotic breeds

PLoS One
PMCID: 5919407
PMID: 29698497
DOI: 10.1371/journal.pone.0196276
call_split See protocol

[…] ed using the software package TreeView version 1.6.6 []. Bootstrap values were obtained with 1,000 replicates over the loci.The hierarchical analysis of molecular variance (AMOVA) was performed using ARLEQUIN software version 3.5 [] in order to quantify the degree of differentiation among populations.Population structure across the entire dataset was analysed using a Bayesian approach implemented […]


Hidden diversity: Phylogeography of genus Ototyphlonemertes Diesing, 1863 (Ototyphlonemertidae: Hoplonemertea) reveals cryptic species and high diversity in Chilean populations

PLoS One
PMCID: 5919620
PMID: 29698411
DOI: 10.1371/journal.pone.0195833

[…] formed after the species delimitation were in accord with these results. Therefore, the populations considered here are the ones delimited in such analyses.The population analyses were performed with Arlequin v3.5 software []. The parameters used to describe genetic diversity at each locality and each marker were the number of polymorphic sites (S), haplotype diversity (h) [], the nucleotide diver […]


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Arlequin institution(s)
CMPG, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland

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