Arlequin ver 3.5.2.2
(released on 02.08.2015)
| About | What's new | Implemented methods | Downloads | Screenshots |
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Arlequin ver 3.5.2.2(released on 02.08.2015) |
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| 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 |
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| 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 |
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| Haplotype frequency estimation | Estimates
the frequency of haplotypes present in the population by maximum
likelihood methods |
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| Gametic phase estimation | Estimates
the most like gametic phase of multi-locus genotypes using a
pseudo-Bayesian approach (ELB algorithm) |
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| Linkage disequilibrium | Test
of non-random association of alleles
at different loci |
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| Hardy-Weinberg equilibrium | Test
of non-random association of alleles
within diploid individuals |
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| Tajima’s neutrality test | Test
of the selective neutrality of a
random sample of DNA sequences or RFLP haplotypes under the infinite
site model |
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| Fu's neutrality test | Test
of the selective neutrality of a
random sample of DNA sequences or RFLP haplotypes under the infinite
site model |
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| 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 |
| 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 |
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| FST-Pairwise genetic distances | FST-based
genetic distances for short
divergence time |
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| 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 |
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| Assignment test of genotypes | Assignment
of individual genotypes to
particular populations according to estimated allele frequencies |
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| 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. |
| Correlations or partial correlations between a set of 2 or 3 matrices | Can be used to test for the presence of isolation-by-distance |
| 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 |