Frequency by Pop [AFP]: Outputs allele frequencies at each locus by population.
Graph All Loci [AGL]: Provides a single graph of locus by locus allele frequency
data. For large datasets this output can take some time, and it may be preferable to skip
this option
Graph by Locus [AGF]: Provides individual locus graphs of Allele Frequency Data.
For large datasets this output can take some time, and it may be preferable to skip this
option
Graph by Pop for each Locus[AGP]: Provides individual worksheets for each locus.
Each worksheet provides an individual pie chart of allele frequencies for each
population.
Frequency by Locus [AFL]: Outputs allele frequencies in each population with loci in
columns. For microsatellite datasets (with alleles coded by size in base pairs), this
option produces a table with the number of rows equal to the number of distinct allele
sizes across the range encountered in the whole dataset. For such datasets, often with
certain allele sizes missing, output can take some time.
Tip: The tabled data provide a good visual indication of size distribution of alleles, and
size overlap between loci, and can be a useful tool for planning the multiplexing of
different loci. The Allele list is an alternative for this.
Het, Fstat & Poly by Pop [HFP]: Outputs for each population in rows: number of samples
(N), the number of alleles (Na), the effective number of alleles (N
e
), the information
index (I), the observed (H
o
), expected (H
e
) and unbiased expected heterozygosity (uH
e
),
and Fixation index (F). This option also outputs the mean over loci and the standard
error of each statistic per population along with the grand mean. It also outputs the F
statistics (F
is,
F
st
and F
it
) along with the number of effective migrants (Nm) for each
locus and the mean across loci. The
percentage of polymorphic loci is provided per
population. This is the standard format for most primer note publications.
Het, Fstat & Poly by Locus [HFL]: Outputs the same information as the previous option,
but with loci in columns not rows.
Allelic Patterns [APT]: Summarizes the mean and standard errors across loci for each
population of the following statistics: Number of alleles (Na), Na with frequency >5%,
effective number of alleles (Ne), information index (I), Number of private alleles,
Number of Locally Common alleles (frequency >=5%) found in <=25% and <=50% of
populations, expected heterozygosity (He) and unbiased expected heterozygosity (uHe).
Graph Pattern [APT]: Provides graphical output of the above information.
Allele list [ALI]: Tallies for each locus the occurrence of all distinct allele sizes across the
range encountered in the whole dataset.
Tip: This is a useful tool for planning the multiplexing of different loci.
Private alleles list [PAS] & [PAL]: Outputs to sheet [PAS] a list of the private alleles by
population, and outputs to sheet [PAL] a list of the samples containing one or more
private alleles. This is in standard GenAlEx format for further analyses if required.
Nei Distance: Outputs the pairwise population Nei’s Genetic Distance and Nei’s Genetic
Identity.
Nei Unbiased Distance: Outputs the pairwise Nei’s Unbiased Genetic Distance and Nei’s
Genetic Identity between populations.