GDA
documentation

Version 1.1 (7 January 2002)
Computes linkage and hardy-weinberg disequilibrium, some genetic distances, and provides method-of-moments estimators for hierarchical F-statistics.

• Windows
• Mac OS 10.2.8 and 10.3 (Jaguar and Panther)

• AFLP……..

• uses NEXUS file format

• If a token begins with a single or double quote character, then every character until the next, matching quote character will be treated as a single token. This is useful as a means of putting blank spaces insice poulation or locus lables.
• commands:
  • begin
  • dimensions
  • format
  • locusallelelabels
  • matrix
  • end

#nexus

begin gdadata; [comments are surrounded by square brackets]
  dimensions npops=2 nloci=3;
  format missing=? seperator=/;
  locusallelelabels
    1 'pgi 1',
    2 'pgi 2',
    3 adh / slow fast
  ;
  matrix
    Embudo:
      indiv_1 A/A 100/100 slow/fast
      indiv_2 A/A 75 / 90 slow/slow
      indiv_3 A/a 75/100  fast/Slow
      indiv_4 A/A 100/100 fast/fast,
    Black_Mesa:
      1 a/a 110/100 fast/slow
      2 a/A  75/100 slow/slow
      3 a/a 100/100 fast/fast
  ;
end;

• Lewis, P. O., and Zaykin, D. 2001. Genetic Data Analysis: Computer program for the analysis of allelic data. Version 1.0 (d16c). Free program distributed by the authors over the internet from http://lewis.eeb.uconn.edu/lewishome/software.html