PDF | Documentation for Arlequin Software Manual | ResearchGate, the professional network for scientists. Manual Arlequin ver 2. ARLEQUIN ver A software for population genetic data analysis. Authors: Stefan Schneider, Jean-Marc Kueffer, David Roessli. An Interated Software Packae for Population Genetics Copyriht Laurent Excoffier. All rihts reserved. 2 Manual Arlequin ver 3. ARLEQUIN VER 3.

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How to et the last version of the Arlequin software? Preparin input files Definin the Genetic Structure to be tested 0. Format of Arlequin input files 5 3. Project file structure 5.

Table of contents Profile section Data section Haplotype list optional Distance matrix optional Samples Genetic structure Mantel test settins Example of an input zrlequim Automatically creatin the outline of a project file Conversion of data files Arlequin batch files 39 4 Output files 4 4. Result file 4 4. Table of contents Haplotype inference Haplotypic data or Genotypic data with known Gametic phase Genotypic data arlequi, unknown Gametic phase EM alorithm EM zipper alorithm ELB mannual Linkae disequilibrium between pairs of loci Exact test of manuual disequilibrium haplotypic data Likelihood ratio test of linkae disequilibrium enotypic data, ametic arrlequim unknown Measures of ametic disequilibrium haplotypic data Hardy-Weinber equilibrium Neutrality tests Ewens-Watterson homozyosity test Ewens-Watterson-Slatkin exact test Chakraborty’s test of population amalamation Tajima’s test of selective neutrality Fu s F S test of selective neutrality 8 7.

Inter-population level methods Population enetic structure inferred by analysis of variance AMOVA Haplotypic data, one roup of populations Haplotypic data, several roups of populations Genotypic data, one roup of populations, no within- individual level Genotypic data, several roups of populations, no within- individual level Genotypic data, one population, within- individual level Genotypic data, one roup of populations, within- individual level Genotypic data, several roups of populations, within- individual level Minimum Spannin Network MSN amon haplotypes Locus-by-locus AMOVA Population specific F ST indices Population pairwise enetic distances Reynolds distance Reynolds et al.

Arleqiim s linearized F ST ‘s Slatkin Overview of input file keywords 4. Arlequin is the French translation of “Arlecchino”, a famous character of the Italian “Commedia dell’arte”. As a character he has many aspects, but he has the ability to switch amon them very easily accordin to its needs and to necessities.

This polymorphic ability is symbolized by his colorful costume, from which the Arlequin icon was desined.

Arlequin philosophy The oal of Arlequin is to provide the averae user in population enetics with quite a lare set of basic methods and statistical tests, in order to extract information on enetic and demoraphic features of a collection of population samples. The raphical interface is desined to allow users to rapidly select the different analyses they want to perform on their data. We felt important to be able to explore the data, to analyze several times the same data set from different perspectives, with different selected options.

The statistical tests implemented in Arlequin have been chosen such as to minimize hidden assumptions and to be as powerful as possible. Thus, they often take the form of either permutation tests or exact tests, with some exceptions.

Finally, we wanted Arlequin to be able to handle enetic data under many different forms, and to try to carry out the same types of analyses irrespective of the format of the data. Because Arlequin has a rich set of features and many options, it means that the user has to spend some time in learnin them. However, we hope that the learnin curve will not be that steep.


Arlequin is made available free of chare, as lon as we have enouh local resources to support the development of the proram. In this manual, we have tried to provide a description of The data types handled by Arlequin The way these data should be formatted before the analyses 3 The raphical interface 4 The impact of different options on the computations. Introduction 8 5 Methodoloical outlines describin which computations are actually performed by Arlequin.

Even thouh this manual contains the description of some theoretical aspects, it should not be considered as a textbook in basic population enetics. We stronly recommend you to consult the oriinal references provided with the description of a iven method if you are in doubt with any aspect of the analysis. The basic data types are: This haplotypic form can result from the analyses of haploid enomes mtdna, Y chromosome, prokaryotesor from diploid enomes where the ametic phase could be inferred by one way or another.

Note that allelic data are treated here as a sinle locus haplotype. Haplotypic standard HLA data: Each enotype is entered on two separate lines, with the two alleles of each locus bein on a different line.

Genotypic DNA sequence data: The ametic phase of a multi-locus enotype may be either known or unknown.

If the ametic phase is known, the enotype can be amnual as made up of two well-defined haplotypes. For enotypic data with unknown ametic phase, you can consider the two. Introduction 9 alleles present at each locus as codominant, or you can allow arlequimm the presence of a recessive allele.

This manuxl finally four possible forms of enetic data: Haplotypic data, Genotypic data with known ametic phase, Genotypic data with unknown ametic phase no recessive alleles Genotypic data with unknown ametic phase recessive alleles.

Each nucleotide is considered as a distinct locus. The four nucleotides “C”, “T”, “A”, “G” are considered as unambiuous alleles for each locus, and the “-” is used to indicate a deleted nucleotide.

Usually the question mark “? The followin notation for ambiuous nucleotides are also reconized: Each restriction site is considered as a distinct locus. The presence of a restriction site should be coded as a “”, and its absence as a “0”. The “-” character should be arleequim to denote the deletion of a site, not its absence due to a point mutation.

For each locus, one should provide the number of repeats of the microsatellite motif as the allelic definition, if one wants his data to be analyzed accordin to the step-wise mutation model for the analysis of enetic structure.

It may occur that the absolute number of repeats is unknown. If the difference in lenth between amplified aarlequim is the direct consequence of chanes in repeat numbers, then the minimum lenth of the amplified product could serve as a reference, allowin to.

Introduction 0 code the other alleles in terms of additional repeats as compared to this reference. If this stratey aarlequim impossible, then any other number could be used as an allelic code, but the stepwise mutation model could not be assumed for these data.

Standard data haplotypes are thus compared for their content at each locus, without takin special care about the nature mwnual the alleles, which can be either similar or different. Population samples are then only compared for their allelic frequencies.

In the first cateory statistical information is extracted independently from each population, whereas in the second cateory, samples are compared to each other.


Some diversity measures like the number of polymorphic sites, ene diversity.

The distribution of the number of pairwise differences between haplotypes, from which parameters of a demoraphic NEW or spatial population expansion can be estimated Estimates the frequency of haplotypes present in the population by maximum likelihood methods. Estimates the most like ametic phase of multi-locus enotypes usin a pseudo- Bayesian approach ELB alorithm. Test of non-random association of alleles at different loci. Test of non-random association of alleles within diploid individuals.

DnaSP and Arlequin

Tests of selective neutrality based on Ewens samplin theory under the infinite alleles model. A test of selective neutrality and population homoeneity. This test can be used when sample heteroeneity is suspected. This tree can also be computed for all the haplotypes found in different populations if activated under the AMOVA section. Comparison of population samples for their haplotypic content. All the results are then summarized in a table. Different hierarchical Analyses of Molecular Variance to evaluate the amount of population enetic structure.

F ST based enetic distances for short diverence time. Test of non-random distribution of haplotypes into population samples under the hypothesis of panmixia. Assinment test of enotypes Assinment of individual enotypes to particular populations accordin to estimated allele frequencies. Correlations or partial correlations between a set of or 3 matrices Short description: Can be used to test for the presence of isolation-by-distance.

At least 0Mb free hard disk space. Arlequin 3 installation Download Arlequin3. Extract all files contained in Arlequin3.

Arlequin ver

Arlequin 3 uninstallation Simply delete the directory where you installed Arlequin. The reistries were not modified by the installation of Arlequin. This script needs if files.

However, a few parameters are limited to values within the rane shown below. Introduction 5 Other limitations: Line lenth in input file is limited to 00, characters Interleaved format is not supported in Arlequin.

This concerns haplotype definition, multilocus enotypes, and distance matrices. Schneider Arlequin ver. An interated software packae for population enetics data analysis.

Arlequin will be updated reularly and can be freely retrieved on What’s new in version Version 3. Therefore Arlequin does not rely on Java anymore. This has two consequences: At the moment we release a Windows versionXP, and. Introduction 6 above and we shall probably release later a Linux. Support for the Mac has been discontinued. Other main chanes include:. Correction of many small bus.

Incorporation of two new methods to estimate ametic phase and haplotype frequencies a. An extension of the EM alorithm allowin one to handle a larer number of polymorphic sites than the plain EM alorithm. Incorporation of a least-square approach to estimate the parameters of an instantaneous spatial expansion from DNA sequence diversity within samples, and computations of bootstrap confidence intervals usin coalescent simulations. Estimation of confidence intervals for F-statistics, usin a bootstrap approach when enetic data on more than 8 loci are available.

Update of the java-script routines in the output html files, makin them fully compatible with Firefox. A completely rewritten and more robust input file parsin procedure, ivin more precise information on the location of potential syntax and format mistakes. Use of the ELB alorithm described above to enerate samples of phased multilocus enotypes, which allows one to analyse unphased multi-locus enotype data as if the phase was known.

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