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 multilocus genotypes using a
pseudoBayesian approach (ELB algorithm)

Linkage disequilibrium 

Test
of nonrandom association of alleles
at different loci

HardyWeinberg
equilibrium 

Test
of nonrandom 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

EwensWatterson
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 