Arlequin protocols

View Arlequin computational protocol

Arlequin statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.


Citations per year

Citations chart

Popular tool citations

chevron_left Haplotype network construction chevron_right
Popular tools chart

Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

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


Add your version



  • person_outline Laurent Excoffier <>

Publications for Arlequin

Arlequin in pipelines

PMCID: 5817159
PMID: 29468047
DOI: 10.1002/ece3.3821

[…] in genetix 4.05.2 (belkhir, borsa, chikhi, raufaste, & bonhomme, ) from the same snp dataset., pairwise population f st values were estimated among populations inferred from these analyses using arlequin (excoffier & lischer, ). also, the contribution of loci under selection on the observed population structure was assessed by identification of f st outlier loci using bayescan […]

PMCID: 5817159
PMID: 29468047
DOI: 10.1002/ece3.3821

[…] will aid in combating the dearth of genetic data available for labeobarbus and other cyprinids., raw sequence data, processed input files for the final dataset (structure, genepop, fineradstructure, arlequin, genetix, diyabc, geste/bayescan, and vcf), and regular expressions for removing adapter pollution are available from the dryad digital repository:, p.b. […]

PMCID: 5301200
PMID: 28186200
DOI: 10.1038/srep42416

[…] in ). all loci were tested for conformity with hardy-weinberg equilibrium using the randomization test implemented in genepop and were also tested for neutrality using the ewens-watterson test in arlequin v3. rates of allelic dropout (ado) and false alleles (fa) were estimated according to broquet and petit (2004). allelic richness (ar) was calculated using fstat. statistical significance […]

PMCID: 5459329
PMID: 28582394
DOI: 10.1371/journal.pone.0178001

[…] verified using genepop v. 4.3 [, ]., genetic boundaries between populations were inferred using barrier software version 2.2 []. for genetic population structure, fst values were calculated using arlequin v. to investigate the pattern of population structure, the software structure v.2.3.4 [] was used to identify clusters of genetically similar populations based on bayesian approach. […]

PMCID: 5721624
PMID: 29216823
DOI: 10.1186/s12862-017-1089-6

[…] and stutter were assessed using microchecker 2.23 []., for the plastid rbc spacer, number of haplotypes (n h), haplotype (h) and nucleotide (π) diversity were estimated for each locality using arlequin 3.5 []. this program was also applied to calculate pairwise values of genetic differentiation (f st). all results for significance of covariance components were tested using 105 […]

To access a full list of citations, you will need to upgrade to our premium service.

Arlequin in publications

PMCID: 5919407
PMID: 29698497
DOI: 10.1371/journal.pone.0196276

[…] 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 […]

PMCID: 5917027
PMID: 29695730
DOI: 10.1038/s41598-018-24497-7

[…] we grouped all mitochondrial genomes by sub-species and sample type (historical or modern sample) and calculated haplotype statistics, molecular diversity indices, and neutrality tests in arlequin3.5. we assessed the effect of unequal sample size by using permutation tests. to this end, we randomly subsampled mitochondrial genomes from each population to match the population […]

PMCID: 5941139
PMID: 29765588
DOI: 10.1093/aobpla/ply026

[…] just the core dna barcode loci. for plastid data, haplotypes were determined from nucleotide substitutions and indels of the aligned sequences. basic population genetic statistics were performed in arlequin version 3.0 (), and this included the number of haplotypes, as well as hierarchical amova in groups according to: (i) ploidy level (diploid vs. tetraploid); (ii) geographic regions (wales, […]

PMCID: 5921438
PMID: 29699488
DOI: 10.1186/s12862-018-1178-1

[…] values were used to compute a principal coordinate analysis (pcoa in r package ape version 3.5 ( a locus-by-locus analysis of molecular variance (amova) was performed on arlequin v3.5.2 [] to test for genetic differentiation (fct) between arrangements at each specific polymorphic site. a hierarchical structure was considered with two groups corresponding to the two […]

PMCID: 5905111
PMID: 29665772
DOI: 10.1186/s12711-018-0388-8

[…] variation and genetic differentiation between populations by performing 10,000 permutations. in addition, computed pairwise comparisons of fst values with 1000 permutations were obtained with arlequin v3.1 []., to establish genealogical relationships between haplotypes and their frequencies, a haplotype network was constructed using the median-joining method [] with the software network […]

To access a full list of publications, you will need to upgrade to our premium service.

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

Arlequin reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Arlequin