GDA

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)

• Microsat
• RFLP
• AFLP
• SNP
• Standard (multi-allelic marker)

• 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:
    • number of populations: npops=2
    • number of loci: nloci=5
  • format:
    • tokens / notokens
    • labels / nolables
    • interleaved
    • haploid
    • missing=?
    • separator=/
    • datapoint=standard
  • locusallelelabels (optional):
    • loci names
    • allele names can be provided
    • loci will be numbered beginning with 1 if this command is absent
  • matrix:
    • end of the data for one population is signified by either a comma or the semicolon indicating the end of the matrix command
  • end
• not case-sensitive, except in the matrix command (allele named A is treated as being distinct form a)

• two ways:
  • if all loci are haploid: include the keyword haploid in the format command
  • mixture of haploid and diploid data: hapset command is used to specify which loci are haploid

• diploid data:

  #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;

• haploid data:

  #nexus
  
  begin gdadata;
  	dimensions nloci=5 npops=2;
  	format haploid tokens missing=? datapoint=standard;
  	locusallelelabels 
  		1 locus_1 [ / 1 2 3 4], 
  		2 locus_2 [ / 1 2 3 4], 
  		3 locus_3 [ / 1 2 3 4], 
  		4 locus_4 [ / 1 2 3 4], 
  		5 locus_5 [ / 1 2 3 4];
  	matrix
  	Pop_1:	_1_ 4 3 3 3 4
  		_2_ 4 4 3 3 4
  		_3_ 4 4 3 3 4
  		_4_ 4 4 ? 3 4
  		_5_ 4 4 2 4 4
  		_6_ 4 4 4 4 4
  		_7_ 4 4 3 4 4
  		_8_ 4 4 3 4 4
  		_9_ 4 4 ? 3 4
  		10_ 4 4 3 3 4,
  	Pop_2:	_1_ 4 4 2 2 4
  		_2_ 4 3 4 3 4
  		_3_ 4 4 3 3 4
  		_4_ 4 4 4 4 4
  		_5_ 4 3 4 4 4
  		_6_ 4 4 4 2 4
  		_7_ 4 4 3 3 4
  		_8_ 4 4 4 4 4
  ;
  end;

• mixed haploid/diploid data:

  #NEXUS
  
  [Note: first 5 loci are diploid and last 3 are haploid]
  
  begin gdadata;
    dimensions nloci=8 npops=6;
    format tokens labels missing=? datapoint=standard;
    hapset 6-8;
    locusallelelabels
      1 'dip 1',
      2 'dip 2',
      3 'dip 3',
      4 'dip 4',
      5 'dip 5',
      6 'hap 1',
      7 'hap 2',
      8 'hap 3'
    ;
    matrix
      Pop1:
        indiv1 4/4 4/3 4/3 3/3 4/4 3 3 4
        indiv2 4/4 4/4 4/3 3/3 4/4 3 3 4
        ...

• 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