Arlequin (version 3.0): An integrated software package for population genetics data analysis

Abstract

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 http://cmpg.unibe.ch/software/arlequin3.

Frequency analysis of HLA class I alleles in Iranian patients with progressive and non-progressive chronic lymphocytic leukemia

“…Allele frequencies in CLL patients and controls were calculated by direct counting. Two-locus haplotype (HLA-A/B) frequencies in patients and healthy controls were estimated by maximum-likelihood method according to the expectation-maximization algorithm using Arlequin 2.0 [29].…”

Temporal differentiation across a West-European Y-chromosomal cline: genealogy as a tool in human population genetics

“…All values were estimated using ARLEQUIN v.3.1 23 and tested for statistical significance by means of random permutation of samples in 10 000 replicates. For the pairwise F ST -values, the sequential Bonferroni correction was applied to correct significance levels for multiple testing.…”

Diverse genetic origin of Indian Muslims: evidence from autosomal STR loci

“…52 Arlequin software package Version 3.1 53 was used to determine HardyWeinberg P-values, observed heterozygosity (H o ), expected heterozygosity (He) and gene diversity (GD) values. Locus-wise GD and polymorphic information content were computed using Power Marker V3.25.…”

“…Genetic structuring among Indian Muslims was determined through hierarchical analysis of molecular variance by grouping them according to their sect (Shia and Sunni) and geographic location (north, west and south) using Arlequin Version 3.1. 53 The allele frequencies of the 13 STR markers for the complied populations (Supplementary Table S1) were prearranged and used to generate NJ trees based on Nei's D A genetic distances using various options in the PHYLIP 3.6 software. 55 Initially, bootstrapping of STR alleles was carried out with 1000 replications by the option SEQBOOT, and then the GENDIST option was used to calculate Nei's D A genetic distances for the acquired multiple data sets of 1000 bootstrap matrices.…”

“…56 Various components of genetic variance, such as coefficient of gene differentiation (Gst), total GD (Ht) and GD within population (Hs) were calculated using DISPAN software. 57 Locus-wise exact test of population differentiation was performed using Arlequin Version 3.1 53 to analyze the extent of genetic diversity among the Indian Muslims and their geographically closest neighboring Hindu (including several caste and tribal populations) populations at the analyzed 13 STR loci.…”