Genetic Data Analysis Software
All programs run under MSWindows unless otherwise
indicated. Most programs can be freely downloaded from the Internet.
- tests for deviations from Hardy Weinberg equilibrium due to stuttering and
large allele drop out, and provides adjusted genotype frequencies. Accepts
- Add-In for Excel which has a variety of features useful for genetic analysis.
Especially useful is a suite of resampling and permutation procedures.
TOOLKIT - Add-In for Excel which checks data and brings them into input
file format for commonly used programs, including GENEPOP and FSTAT.
Primer Design and Restriction Mapping
Relatedness and Parentage
- Likelihood-based parentage inference using codominant marker data.
(Mac) - calculates average genetic relatedness and its confidence limits between
pairs or groups of indiviudals identified by demographic variables.
(Mac) - calculates expected frequency distribution of relatedness values of
specific relationships (full sib, half sib), and tests the likelihood of a
pair of individuals belonging to a specific relationship.
(scroll to the bottom): Maximum likelihood assignment of offspring to known
parents from multilocus data.
- Partitions groups of individuals into groups of full and half sibs.
Infers parental genotypes and calculates parental contributions.
- calculates the probability of detecting multiple matings in a sample of
offspring, depending on genetic diversity and parental contribution.
- Powerful genetic analysis packages performing a wide variety of tests, including
hierarchical analysis of variance. Has import feature for GENEPOP files. May
give spurious results if input contains a lot of missing data.
- Detection of historical population bottlenecks from allele frequency data.
- Analysis of nucleotide polymorphism from aligned DNA sequence data. Very
useful for population genetic analyses of sequence data, including tests for
Calculates FST, RST and tests the estimates, among other standard population
genetics statistics. Also produces and tests pairwise FST values. New and
useful feature is the estimation of allelic richness corrected for sample
size, and tests for differences in genetic diversity between groups of samples.
- Program for the analysis of discrete genetic data, based on Weir (1996)
Genetic Data Analysis
- Excel Add-In for the analysis of genetic data. Particularly useful for dominant
data such as RAPD and AFLP data.
- performs exact tests for deviation from Hardy-Weinberg, linkage disequilibrium,
population differentiation and isolation by distance (DOS). There is also
a web based
version of the program.
Powerful analysis package for population genetics, but you have to understand
French. Has nice features such as a PCA on individual genotypes and permutation
tests of FST.
Package of programs for computing population parameters, such as population
size, population growth rate and migration rates by using likelihoods over
all possible gene genealogies for samples of data (sequences, microsatellites,
and electrophoretic polymorphisms) from populations
. Includes Coalesce,
- Program for microsatellite analysis (distances, Fst, Rst), which has been
compiled for both DOS and Mac
- Maximum likelihood estimation of Ne with simultaneous estimation of immigration
from another population.
ESTIMATOR - uses three different methods of Ne estimation. Accepts GENEPOP
and ARLEQUIN input files.
Principal component analysis on allele frequency data with significance testing.
- Windows (3.1, 95, NT) program for the analysis of genetic variation among
and within populations using co-dominant and dominant markers, and quantitative
- DOS package for the analysis of (mtDNA) RFLP data. Old and tested. Provides
haplotype and nucleotide diversity, nucleotide divergence and acrries out
Monte Carlo tests for differences in haplotype frequencies.
- DOS program for the analysis of microsatellite data. Calculates a variety
of statistics assuming stepwise mutation models.
- uses a clustering method to identify population structure and assigns individuals
to those populations. No a priori division into samples required.
- Tools for Population Genetic Analysis. Can perform hierarchical analyses
and use dominant data.
Assignment tests and Mixed stock analysis
(scroll to the bottom of this page)
- Allocation of individuals to populations from AFLP data
- Windows 95/NT program for assignment and exclusion of individuals to/from
populations. Similar, but more extended stats to DOH (see above) and IMMANC
- A program that calculates the probability that an individual is an immigrant,
or has recent immigrant ancestry, using the multilocus genotype
- Population assignment of individuals based on multilocus genotype data.
Several different methods, including Maximum Likelihood and Jackknifing. Accepts
GENEPOP files and prepares input files for SPAM.
- Uses genotype data to identify the loci most useful for population
assignment. Takes GENEPOP files.
- Statistics Package for Analyzing Mixtures. Advanced mixed stock analysis
using Likelihood and Bayesian statistics. Input files can be prepared using
Sequence alignment and editing
Molecular Evolutionary Genetics Analysis - reconstructs phylogenies using
distance matrices and maximum parsimony methods, and includes neighbour joining,
branch-and-bound parsimony methods and bootstrapping. The manual is available
in HTML format.
4.0: The long awaited phylogeny program - still a beta version, but it's
on sale from Sinauer
Assoc. MMBL has PAUP, if you want to use it.
Inference Package - PHYLIP: Extensive package of programs for inferring
phylogenies for Windows. Sometimes clumsy in data handling, but fast, versatile
Software package for data analysis in molecular biology and evolution.