Genetic Data Analysis Software

All programs run under MSWindows unless otherwise indicated. Most programs can be freely downloaded from the Internet.

General Utilities

• MICROCHECKER - tests for deviations from Hardy Weinberg equilibrium due to stuttering and large allele drop out, and provides adjusted genotype frequencies. Accepts GENEPOP files.
• POPTOOLS - Add-In for Excel which has a variety of features useful for genetic analysis. Especially useful is a suite of resampling and permutation procedures.
• MICROSATELLITE 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

• PRIMER DESIGN SOFTWARE LINKS
• GENERUNNER - Multiuse program which also designs primers and finds restriction enzymes cutting at specific sequences.
• PRIMER3 - Web based software for primer design
• WEBCUTTER - an on-line tool for restriction mapping nucleotide sequences
• Qiagen Oligo Analysis and Plotting Tool - simple but useful tool to calculate primer parameters (melting temperature, molecular weight, GC content) and to test for primer-dimers.

Relatedness and Parentage

• CERVUS - Likelihood-based parentage inference using codominant marker data.
• RELATEDNESS (Mac) - calculates average genetic relatedness and its confidence limits between pairs or groups of indiviudals identified by demographic variables.
• KINSHIP (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.
• PAPA (scroll to the bottom): Maximum likelihood assignment of offspring to known parents from multilocus data.
• PARENTAGE - Partitions groups of individuals into groups of full and half sibs. Infers parental genotypes and calculates parental contributions.
• PRDM - calculates the probability of detecting multiple matings in a sample of offspring, depending on genetic diversity and parental contribution.

Population Genetics

• ARLEQUIN - 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.
• BOTTLENECK - Detection of historical population bottlenecks from allele frequency data.
• DNASP - Analysis of nucleotide polymorphism from aligned DNA sequence data. Very useful for population genetic analyses of sequence data, including tests for selection.
• FSTAT: 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.
• GDA - Program for the analysis of discrete genetic data, based on Weir (1996) Genetic Data Analysis
• GENAlEx - Excel Add-In for the analysis of genetic data. Particularly useful for dominant data such as RAPD and AFLP data.
• GENEPOP - 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.
• GENETIX: 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.
• LAMARC: 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, Fluctuate, Migrate and Recombine.
• MICROSAT - Program for microsatellite analysis (distances, Fst, Rst), which has been compiled for both DOS and Mac
• MLNE - Maximum likelihood estimation of Ne with simultaneous estimation of immigration from another population.
• NE ESTIMATOR - uses three different methods of Ne estimation. Accepts GENEPOP and ARLEQUIN input files.
• PCAGEN: Principal component analysis on allele frequency data with significance testing.
• POPGENE - Windows (3.1, 95, NT) program for the analysis of genetic variation among and within populations using co-dominant and dominant markers, and quantitative data.
• REAP - 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.
• RSTCalc - DOS program for the analysis of microsatellite data. Calculates a variety of statistics assuming stepwise mutation models.
• STRUCTURE - uses a clustering method to identify population structure and assigns individuals to those populations. No a priori division into samples required.
• TFPGA - Tools for Population Genetic Analysis. Can perform hierarchical analyses and use dominant data.

Assignment tests and Mixed stock analysis

• AFLPOP (scroll to the bottom of this page) - Allocation of individuals to populations from AFLP data
• GENECLASS - Windows 95/NT program for assignment and exclusion of individuals to/from populations. Similar, but more extended stats to DOH (see above) and IMMANC (see below).
• IMMANC - A program that calculates the probability that an individual is an immigrant, or has recent immigrant ancestry, using the multilocus genotype
• WHICHRUN - 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.
• WHICHLOCI - Uses genotype data to identify the loci most useful for population assignment. Takes GENEPOP files.
• SPAM - Statistics Package for Analyzing Mixtures. Advanced mixed stock analysis using Likelihood and Bayesian statistics. Input files can be prepared using WhichRun.

Phylogenetics

Link collections

• Other Phylogeny Programs by Joe Felsenstein here at U of Washington. Very extensive and regularly updated. To good to be reproduced, so below are only some of the programs I know better myself.
• Software links at the University of Glasgow, including programs for tree building and sequence alignment.

Sequence alignment and editing

• CLUSTAL-one of the most widely used and powerful multiple alignment programs. Documentation, download, read the manuscript and online help (Strasbourg) from Finnish EMBnet node.
• BioEdit: Sequence alignment editor featuring automated links to ClustalW and BLAST, as well as to relevant websites. Very useful.

Specific Programs

• MEGA: 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.
• PAUP* 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.
• PHYlogeny Inference Package - PHYLIP: Extensive package of programs for inferring phylogenies for Windows. Sometimes clumsy in data handling, but fast, versatile and powerful.
• DAMBE: Software package for data analysis in molecular biology and evolution.