====== GDA ======
**[[http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php|GDA]]**\\
{{gdahelp.pdf|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.

===== 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 =====
  * uses [[NEXUS]] file format


==== 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: <code>
#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;
</code>

  * haploid data: <code>
#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;
</code>

  * mixed haploid/diploid data:<code>
#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
      ...
</code>



===== How to cite =====
  * 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