Contents

5. Components of Genetic Variation

• Epistasis
  • Extension to haploids and polyploids
• Linkage
  • Estimation of gametic-phase disequilibrium
  • Mapping gene loci
  • Effect of linkage on the genetic variance of quantitative characters

Programs

• GDA: Software for the Analysis of Discrete Genetic Data. GDA, a Microsoft Windows program (by Paul Lewis, University of Conn.) for analyzing discrete genetic data, includes exact tests for disequilibrium. More details can be found at the GDA WWW site .

• Mathematica workbook for computing epistatic variances and the complete (A,D, AxA, AxD, DxD) genetic decomposition for two diallelic loci, as detailed on pages 85-92 and (especially) Example 2.

• Fastlink v 2.2 (aka LINKAGE v 5.1) is a program for constructing fast linkage maps.
  • Fastlink v 2.2 FTP site
  • More information

• Linkage analysis ftp site at Columbia contains a varitey of programs and other information very useful to linkage analysis, especially in humans.
  • The main Columbia site
  • Back issues of the linkage newletters
  • Additions/corrections to Ott's Linkage analysis book
  • Software maintained at this ftp site.

Programs

• Tools for Population Genetic Analyses (TFPGA): A Windows program (by Mark Miller at Northern Arizona University) for the analysis of allozyme and molecular population genetic data. This program calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses. Additional features include the ability to analyze hierarchical data sets as well as data from either codominant markers such as allozymes or dominant markers such as AFLPs or RAPDs. More details can be found at the TFPGA WWW site

• GDA: Software for the Analysis of Discrete Genetic Data. GDA, a Microsoft Windows program (by Paul Lewis, University of New Mexico) for analyzing discrete genetic data, is designed to accompany the second edition of Bruce Weir's book "Genetic Data Analysis" Both 16-bit versions (for Windows 3.1x) and 32-bit versions (for Windows 95 or Windows NT) are available. Includes basic single-locus descriptive statistics, Wright's F-statsistics for subdivided populations, Genetic distance measures, and exact tests for disequilibrium. More details can be found at the GDA WWW site .

• A simple Mathematica program for generating color plots (as a function of allele frequency) of the total, additive and dominance genetic variances, heritability, breeding values, average effects and domiance deviations for a single diallelic locus.

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Bruce Walsh. jbwalsh@u.arizona.edu . Comments welcome.