| 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 |
