Population genetics data analysis program - Arlequin v3.11

Population Genetics statistical program
Arlequin 3.11 (download) & manual download

Homepage =>> http://cmpg.unibe.ch/software/arlequin3


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  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:	Short description:
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 q.
Mismatch distribution	The distribution of the number of pairwise differences between haplotypes, from which parameters of a demographic (NEW in ver 3.x) 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 (NEW in ver 3.x)	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 FS 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:	Short description:
Search for shared haplotypes between populations	Comparison of population samples for their haplotypic content. All the results are then summarized in a table.
AMOVA	Different hierarchical Analyses of Molecular Variance to evaluate the amount of population genetic structure.
Pairwise genetic distances	FST based genetic distances for short divergence time.
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.
Mantel test:	Short description:
Correlations or partial correlations between a set of 2 or 3 matrices	Can be used to test for the presence of isolation-by-distance

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