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Arlequin ver

(released on 02.08.2015)

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Implemented methods

The analyses Arlequin can perform on the data fall into two main categories: intra-population and inter-population methods. In the first category statistical information is extracted independently from each population, whereas in the second category, samples are compared to each other.

Intra-population methods

Standard indices
Some diversity measures like the number of polymorphic sites, gene diversity
Molecular diversity
Calculates several diversity indices like nucleotide diversity, different estimators of the population parameter
Mismatch distribution
The distribution of the number of pairwise differences between haplotypes, from which parameters of a demographic or spatial population expansion can be estimated
Haplotype frequency estimation
Estimates the frequency of haplotypes present in the population by maximum likelihood methods
Gametic phase estimation
Estimates the most like gametic phase of multi-locus genotypes using a pseudo-Bayesian approach (ELB algorithm)
Linkage disequilibrium
Test of non-random association of alleles at different loci
Hardy-Weinberg equilibrium
Test of non-random association of alleles within diploid individuals
Tajima’s neutrality test
Test of the selective neutrality of a random sample of DNA sequences or RFLP haplotypes under the infinite site model
Fu's neutrality test
Test of the selective neutrality of a random sample of DNA sequences or RFLP haplotypes under the infinite site model
Ewens-Watterson neutrality test
Tests of selective neutrality based on Ewens sampling theory under the infinite alleles model
Chakraborty’s amalgamation test
A test of selective neutrality and population homogeneity. This test can be used when sample heterogeneity is suspected
Minimum Spanning Network (MSN)
Computes a Minimum Spanning Tree (MST) and Network (MSN) among haplotypes. This tree can also be computed for all the haplotypes found in different populations if activated under the AMOVA section

Inter-population methods

Search for shared haplotypes between populations
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 genetic structure
FST-Pairwise genetic distances
FST-based genetic distances for short divergence time
Pairwise moecular distances
Molecular distancess between populations based on the number of pairwise differencs between haplotypes
delta-mu square
Genetic distance betwene populations based on microsatellite data
Exact test of population differentiation
Test of non-random distribution of haplotypes into population samples under the hypothesis of panmixia
Assignment test of genotypes
Assignment of individual genotypes to particular populations according to estimated allele frequencies
Detection of loci under selection from F-statistics
Detection of loci under selection by the examination of the joint distribution of FST and heterozygosity under a hierarchical island model.

Mantel test

Correlations or partial correlations between a set of 2 or 3 matrices
Can be used to test for the presence of isolation-by-distance

Site Frequency Spectrum

Computation of the 1D, 2D or multidimensional SFS from DNA data

The SFS files can be used as input for demogrpaphic inference with the program fastsimcoal2.  DNA data must be coded as 0, 1, 2, 3 (for ACGT), where 0 is supposed to be the ancestral state

Last edit:  10.04.2015 by Laurent Excoffier