Masterarbeit, Heidi Lischer

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migrate [2011/07/12 10:50] – heidimigrate [2011/07/14 15:02] (current) – heidi
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   * Microsatellite   * Microsatellite
   * Standard (Electrophoretic marker)   * Standard (Electrophoretic marker)
 +
  
  
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 .... ....
 </code> </code>
-  * interleaved data (not anymore supported by MIGDRAT): <code>+  * interleaved data (not anymore supported by MIGRATE): <code>
 <Number of populations> <number of loci> [project title 0-79] <Number of populations> <number of loci> [project title 0-79]
 <number of sites for locus1> <number of sites for locus 2> ... <number of sites for locus1> <number of sites for locus 2> ...
Line 114: Line 115:
 .... ....
 </code> </code>
 +
 +
 +
 +
  
  
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   * Genotypes   * Genotypes
   * missing data: "?"   * missing data: "?"
-  * can use multi-character coding when you use a delimiter (see the examples for microsatellites)+  * can use multi-character coding when you use a delimiter
   * 2 populations and 11 loci and with 3 or 2 individuals per population: <code>   * 2 populations and 11 loci and with 3 or 2 individuals per population: <code>
  2 11 Migration rates between two Turkish frog populations  2 11 Migration rates between two Turkish frog populations
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  2 11 / Migration rates between two Turkish frog populations  2 11 / Migration rates between two Turkish frog populations
 3 Akcapinar (between Marmaris and Adana) 3 Akcapinar (between Marmaris and Adana)
-PB1058 e/e b/b a/b b/b b/b a/a a/a b/b ?/? c/c Rs/Rf +PB1058    e/e b/b a/b b/b b/b a/a a/a b/b ?/? c/c Rs/Rf 
-PB1059 e/e b/b a/b b/b b/b a/a a/a b/b b/b c/c Rs/Rs +PB1059    e/e b/b a/b b/b b/b a/a a/a b/b b/b c/c Rs/Rs 
-19 +PB1060    e/e b/b b/? b/b a/b a/a a/a b/b b/b c/c Rs/Rs
-PB1060 e/e b/b b/? b/b a/b a/a a/a b/b b/b c/c Rs/Rs+
 2 Ezine (between Selcuk and Dardanelles) 2 Ezine (between Selcuk and Dardanelles)
-PB16843 e/e b/b a/b b/b a/a a/a a/a c/c b/b c/c Rf/Rf +PB16843   e/e b/b a/b b/b a/a a/a a/a c/c b/b c/c Rf/Rf 
-PB16844 e/e b/b b/b b/b a/b a/a a/a c/c b/b c/c Rf/Rs</code>+PB16844   e/e b/b b/b b/b a/b a/a a/a c/c b/b c/c Rf/Rs</code>
  
  
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 #M 2 2 2 #M 2 2 2
 2 Riedtli near Guendelhart-Hoerhausen 2 Riedtli near Guendelhart-Hoerhausen
-0 25.27 137.131 218.218 +0         25.27 137.131 218.218 
-0 27.27 218.216+0         27.27 218.216
 2 Tal near Steckborn 2 Tal near Steckborn
-1 23.25 135.? 218.218 +1         23.25 135.? 218.218 
-1 23.23 135.131 220.218+1         23.23 135.131 220.218
 </code>     </code>    
  
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 50 50
 3 Tallahassee (Mars) 3 Tallahassee (Mars)
-Peter ACACCCAACACGGCCCGCGGACAGGGGCTCGAGGGATCACTGACTGGCAC +Peter     ACACCCAACACGGCCCGCGGACAGGGGCTCGAGGGATCACTGACTGGCAC 
-Donald ACACAAAACACGGCCCGCGGACAGGGGCTCGAGGGGTCACTGAGTGGCAC+Donald    ACACAAAACACGGCCCGCGGACAGGGGCTCGAGGGGTCACTGAGTGGCAC
 Christian ATACCCAGCACGGCCGGCGGACAGGGGCTCGAGGGAGCACTGAGTGGAAC Christian ATACCCAGCACGGCCGGCGGACAGGGGCTCGAGGGAGCACTGAGTGGAAC
 3 St. Marks 3 St. Marks
-Lucrezia ACACCCAACACGGCCCGCGGACAGGGGCTCGAGGGATCACTGACTGGCAC +Lucrezia  ACACCCAACACGGCCCGCGGACAGGGGCTCGAGGGATCACTGACTGGCAC 
-Isabel ACACAAAACACGGCCCGCGGACAGGGGCTCGAGGGGTCACTGAGTGGCAC +Isabel    ACACAAAACACGGCCCGCGGACAGGGGCTCGAGGGGTCACTGAGTGGCAC 
-Yasmine ATACCCAGCACGGCCGGCGGACAGGGGCTCGAGGGAGCACTGAGTGGAAC+Yasmine   ATACCCAGCACGGCCGGCGGACAGGGGCTCGAGGGAGCACTGAGTGGAAC
 </code> </code>
   * not interleaved (2 population with 2 loci): <code>   * not interleaved (2 population with 2 loci): <code>
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 1 4 1 4
 3 3 pop1 3 3 pop1
-ind1 A +ind1      A 
-ind2 A +ind2      A 
-ind3 A +ind3      A 
-ind1 ACAC +ind1      ACAC 
-ind2 ACAC +ind2      ACAC 
-ind3 ACGC+ind3      ACGC
 2 pop2 2 pop2
-ind4 C +ind4      C 
-ind5 C +ind5      C 
-ind4 TGGA +ind4      TGGA 
-ind5 TCGA+ind5      TCGA
 </code> </code>
     * ''H'': HapMap format <code>     * ''H'': HapMap format <code>
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 H 2 2 Make believe data set using simulated data (2 population and 2 loci) H 2 2 Make believe data set using simulated data (2 population and 2 loci)
 3 pop1 3 pop1
-1 A 3 C 0 3+1    A 3 C 0 3
 1000 A 3 T 0 3 1000 A 3 T 0 3
 1010 C 3 G 0 3 1010 C 3 G 0 3
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 1015 C 3 A 0 3 1015 C 3 A 0 3
 2 pop2 2 pop2
-1 A 0 C 2 2+1    A 0 C 2 2
 1000 A 0 T 2 2 1000 A 0 T 2 2
 1010 C 1 G 1 2 1010 C 1 G 1 2
migrate.1310460627.txt.gz · Last modified: 2011/07/12 10:50 by heidi