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.
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Intra-population methods: |
Short description: |
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Standard indices |
Some diversity measures like the number of polymorphic sites, gene diversity. |
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Molecular diversity |
Calculates several diversity indices like nucleotide diversity, different estimators of the population parameter q. |
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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 |
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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 FS 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. |
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Chakraborty’s amalgamation test |
A test of selective neutrality and population homogeneity. This test can be used when sample heterogeneity is suspected. |
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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. |
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Inter-population methods: |
Short description: |
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Search for shared haplotypes between populations |
Comparison of population samples for their haplotypic content. All the results are then summarized in a table. |
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AMOVA |
Different hierarchical Analyses of Molecular Variance to evaluate the amount of population genetic structure. |
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Pairwise genetic distances |
FST based genetic distances for short divergence time. |
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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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Mantel test: |
Short description: |
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Correlations or partial correlations between a set of 2 or 3 matrices |
Can be used to test for the presence of isolation-by-distance |
<ScreenShots>
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