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[Univ. of Edinburgh] A program for population genetic analysis of geographic variation and hybrid zones.
Aqua: Analyzing the Quality
[NMR Spectroscopy Department, Bijovet Center for Biomolecular Research] A suite of programs for analyzing the quality of biomolecular structures that were determined via NMR spectroscopy.
[Univ. of Edinburgh] A program for likelihood-based parentage inference using codominant marker data. It can be used to calculate allele frequencies, run simulation to determine critical values of likelihood ratios, and analyze parentage in populations of animals and plants.
[Mayo Foundation for Medical Education & Research] This software makes disease and genetic marker associations using cases and their parents.
[Lewis & Zaykin] A program for analyzing discrete genetic data.
[GenPak Inc.] Compare whole genomes at the DNA sequence level, looking for identical stretches of bases. Program creates a dotplot, sequence list, and statistics. Download a working version free, or pay for the expensive version.
[MIT] A software package that allows the very rapid extraction of complete multipoint inheritance information from pedigrees of moderate size. This information is then used in exact computation of multipoint LOD scores and in a new method of non-parametric linkage analysis.
[GSF] This software tool detects distance associations between sequence elements.
Map Manager QT
[K. Manly] This program basic functions for entry, editing, and display of quantitative traits and it has three functions for identifying and locating possible quantitative trait loci.
PHYLIP Home Page
[University of Washington] (PHYLogeny Inference Package) “PHYLIP is a package of programs for inferring phylogenies. Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters.”
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[Univ. of Edinburgh] A program for performing analyses of population structure, genetic differentiation, and gene flow using microsatellite data. RSTCALC calculates unbiased estimates of RST and assesses their significance using bootstrap and permutation tests.
[GBF] A database program that compiles data about gene regulatory DNA sequences; from this data programs have been developed to identify putative promoter or enhancer structures.