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gda

GDA

GDA
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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.

Program information

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

Data type handled

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

Input Files

GDADATA block

  • 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)

haploid data

  • 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

example

  • 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
          ...

How to cite

gda.txt · Last modified: 2011/07/13 16:54 by heidi