Arlequin - could be run on Linux

1. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2010.02847.x/full

2. http://popgen.unibe.ch/software/arlequin35/Arl35Downloads.html

3.

Implemented methods

The analyses Arlequin can perform on the data fall into two main categories: intra-population and inter-population methods. In the first categorystatistical 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
AMOVA		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