Masterarbeit, Heidi Lischer

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gda [2008/06/18 10:20] – heidigda [2011/07/13 16:54] (current) – heidi
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   * Windows   * Windows
   * Mac OS 10.2.8 and 10.3 (Jaguar and Panther)   * Mac OS 10.2.8 and 10.3 (Jaguar and Panther)
 +
 +
 +
  
  
  
 ===== Data type handled ===== ===== Data type handled =====
-  * AFLP........+  * Microsat 
 +  * RFLP 
 +  * AFLP 
 +  * SNP 
 +  * Standard (multi-allelic marker)
  
  
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 ===== Input Files ===== ===== Input Files =====
   * uses [[NEXUS]] file format   * uses [[NEXUS]] file format
 +
  
 ==== GDADATA block ==== ==== 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 === === example ===
-<code>+  * diploid data: <code>
 #nexus #nexus
  
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   ;   ;
 end; 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> </code>
  
gda.1213777255.txt.gz · Last modified: 2008/07/22 13:30 (external edit)