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newhybrids [2011/06/03 16:46] heidinewhybrids [2011/06/03 17:20] (current) heidi
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   * Windows   * Windows
 \\ \\
 +
 +
  
  
  
 ===== Data type handled ===== ===== Data type handled =====
 +  * diploid
   * AFLP   * AFLP
   * MICROSAT   * MICROSAT
 +  * Standard
  
 \\ \\
 +
 +
  
  
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 ===== Input Files ===== ===== Input Files =====
-  * whitespace (spaces and or tabs) separated text file *.txt+  * whitespace (spaces and or tabs) separated text file *.txt/*.dat
   * first line: ''NumIndivs '' number of individuals   * first line: ''NumIndivs '' number of individuals
   * second line: ''NumLoci '' number of loci   * second line: ''NumLoci '' number of loci
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       * ''NonLumped'' format: alleles at each locus are given by a consecutive pair of numbers that are white space seperated       * ''NonLumped'' format: alleles at each locus are given by a consecutive pair of numbers that are white space seperated
       * Missing data: ''Lumped'': encoded as ''0'', ''NonLumped'': encoded as ''-1'' (each allele at the missing locus must have a ''-1'')       * Missing data: ''Lumped'': encoded as ''0'', ''NonLumped'': encoded as ''-1'' (each allele at the missing locus must have a ''-1'')
 +
 \\ \\
  
 +==== AFLP data ====
 +  * ''Lumped'' format
 +  * ''+'' band is present
 +  * ''-'' band is absent
 +  * ''0'' missing data
  
 +  * data types can be mixed
  
 +\\
  
  
 +==== Example ==== 
 +  * ''Lumped'' data file: 
 +<code> 
 +NumIndivs 2 
 +NumLoci 6 
 +Digits 1 
 +Format Lumped 
 +LocusNames sAAT1 sAAT2 sAAT3 ADA1 ADA2 ADH 
 +1 11 11 11 0 11 32 
 +2 21 11 21 11 11 12  
 +</code> 
 +  * ''NonLumped'' data file: 
 +<code> 
 +NumIndivs 2 
 +NumLoci 6 
 +Digits 1 
 +Format NonLumped 
 +LocusNames sAAT1 sAAT2 sAAT3 ADA1 ADA2 ADH 
 +1 123 143 -1 -1 144 144 120 122 157 158 144 144  
 +2 135 135 134 140 144 144 120 122 161 161 144 144  
 +</code> 
 +  * AFLP data file (4 Microsat loci, 5 AFLP loci): 
 +<code> 
 +NumIndivs 2 
 +NumLoci 9 
 +Digits 1 
 +Format Lumped 
 +LocusNames m1 m2 m3 m4 A1 A2 A3 A4 A5 
 +1 11 12 13 11 + + + - + 
 +2 22 33 11 22 - - 0 - - 
 +3 12 13 13 11 + - - - + 
 +</code>
  
 ===== How to cite ===== ===== How to cite =====
newhybrids.1307112375.txt.gz · Last modified: 2011/06/03 16:46 (external edit)