Sep 04, 2017 Free Download Arlequin 3.5.2.2 - A handy software solution especially created to provide professionals and students alike with a means of analyzing. Mar 1, 2010 - Abstract. We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute summary statistics (arlsumstat). The command-line versions run under both.

Get expert answers to your questions in Arlequin and Statistical Software and more on ResearchGate, the professional network for scientists. Arlequin philosophy. The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in.

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. Introduction Most genetic studies on non-model organisms require a description of the pattern of diversity within and between populations, based on a variety of markers often including mitochondrial DNA (mtDNA) sequences and microsatellites. The genetic data are processed to extract information on the mating system, the extent of population subdivision, the past demography of the population, or on departure from selective neutrality at some loci.

A series of computer packages have been developed in the last 10 years to assist researchers in performing basic population genetics analyses like Arlequin2 (), DNASP (), FSTAT (), GENEPOP (), or GENETIX (). These programs have been widely used in the molecular ecology and conservation genetics community (;; ). Among these, Arlequin is a very versatile (though not universal) program, and complements the other programs listed above. It can handle several data types like RFLPs, DNA sequences, microsatellite data, allele frequencies, or standard multi-locus genotypes, while allowing the user to carry out the same types of analyses irrespective of the data types. We present here the version 3 of Arlequin with additional methods extending its capacities for the handling of unphased multi-locus genotypes and for the estimation of parameters of a spatial expansion. Note that these new developments are mainly implementations of new methodologies developed in our lab. We believe these methods will be useful to the research community, but we do not claim that alternative methods implemented by other groups in other programs are inadequate.

A new graphical interface has been developed to provide a better integration of the different analyses into a common framework, and an easier exploration of the data by performing a wide variety of analyses with different settings. The tight coupling of Arlequin with the simulation programs SIMCOAL2 (Laval and ) and SPLATCHE () should also make it useful to describe patterns of genetic diversity under complex evolutionary scenarios. T-zero Amiga Download on this page.

⋄ The EM zipper algorithm, which is an extension of the EM algorithm for estimating haplotype frequencies (Excoffier and ), aims at estimating the haplotype frequencies in unphased multi-locus genotypes. The estimation of the gametic phases are a by-product of this process. It proceeds by adding loci one at a time and progressively extending the length of the reconstructed haplo-types.

With this method, Arlequin does not need to build all possible genotypes for each individual like in the conventional EM algorithm, but it only considers the genotypes whose sub-haplotypes have non-null estimated frequencies. It can thus handle a much larger number of polymorphic sites than the strict EM algorithm.

It also gives final haplotype frequencies that often have a higher likelihood than those estimated under the strict EM algorithm, due to the difficulty in exploring the space of all possible genotypes when the number of polymorphic loci in the sample is large. Note that this version of the EM algorithm is equivalent to that implemented in the SNPHAP program by David Clayton fully described on, and whose efficiency for inferring gametic phase has been favorably evaluated (). Estimation of the parameters of a spatial expansion (age of the expansion and deme size scaled by the mutation rate, as well as the number of migrants exchanged between neighbouring demes) from the patterns of polymorphism in a sample of DNA sequences. The estimation is based on a simple model of instantaneous and infinite range expansion, where some time ago, a single deme instantaneously colonized an infinite number of demes subsequently interconnected by migration (as under an infinite-island model) ().