Differences

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--- migrate [2011/07/12 10:45] – heidi
+++ migrate [2011/07/14 15:02] (current) – heidi
@@ Line 24: / Line 24: @@
   * Microsatellite
   * Standard (Electrophoretic marker)
@@ Line 81: / Line 82: @@
 ....
 </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 sites for locus1> <number of sites for locus 2> ...
@@ Line 114: / Line 115: @@
 ....
 </code>
@@ Line 125: / Line 131: @@
   * Genotypes
   * 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:
+  * 2 populations and 11 loci and with 3 or 2 individuals per population: <code>
-<code>
 11 Migration rates between two Turkish frog populations
 Akcapinar (between Marmaris and Adana)
@@ Line 137: / Line 142: @@
 PB16844   ee bb bb bb ab aa aa cc bb cc aa
 </code>
-  * same data but with ''/'' as separator:
+  * same data but with ''/'' as separator: <code>
-<code>
 11 / Migration rates between two Turkish frog populations
 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
+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
 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>
@@ Line 156: / Line 159: @@
   * homozygote individual: needs to be coded as e.g.: 6.6 ("." is the delimiter)
   * missing data: "?’"
-  * Alleles are coded as REPEAT NUMBERS:
+  * Alleles are coded as REPEAT NUMBERS: <code>
-<code>
 3 . Rana lessonae: Seeruecken versus Tal
    Riedtli near Guendelhart-Hoerhausen
@@ Line 169: / Line 171: @@
 </code>
   * Alleles encoded as FRAGMENT LENGTH:
-    * extra line with repeat number, starts with ''#M''
+    * extra line with repeat number, starts with ''#M'' <code>
-<code>
 3 . Rana lessonae: Seeruecken versus Tal
 #M 2 2 2
 Riedtli near Guendelhart-Hoerhausen
-25.27 137.131 218.218
+         25.27 137.131 218.218
-27.27 218.216
+         27.27 218.216
 Tal near Steckborn
-23.25 135.? 218.218
+         23.25 135.? 218.218
-23.23 135.131 220.218
+         23.23 135.131 220.218
 </code>
@@ Line 209: / Line 210: @@
 **examples:**
-  * two populations with a single DNA-locus:
+  * two populations with a single DNA-locus: <code>
-<code>
 1 Make believe data set using simulated data (1 locus)
 Tallahassee (Mars)
-Peter ACACCCAACACGGCCCGCGGACAGGGGCTCGAGGGATCACTGACTGGCAC
+Peter     ACACCCAACACGGCCCGCGGACAGGGGCTCGAGGGATCACTGACTGGCAC
-Donald ACACAAAACACGGCCCGCGGACAGGGGCTCGAGGGGTCACTGAGTGGCAC
+Donald    ACACAAAACACGGCCCGCGGACAGGGGCTCGAGGGGTCACTGAGTGGCAC
 Christian ATACCCAGCACGGCCGGCGGACAGGGGCTCGAGGGAGCACTGAGTGGAAC
 St. Marks
-Lucrezia ACACCCAACACGGCCCGCGGACAGGGGCTCGAGGGATCACTGACTGGCAC
+Lucrezia  ACACCCAACACGGCCCGCGGACAGGGGCTCGAGGGATCACTGACTGGCAC
-Isabel ACACAAAACACGGCCCGCGGACAGGGGCTCGAGGGGTCACTGAGTGGCAC
+Isabel    ACACAAAACACGGCCCGCGGACAGGGGCTCGAGGGGTCACTGAGTGGCAC
-Yasmine ATACCCAGCACGGCCGGCGGACAGGGGCTCGAGGGAGCACTGAGTGGAAC
+Yasmine   ATACCCAGCACGGCCGGCGGACAGGGGCTCGAGGGAGCACTGAGTGGAAC
 </code>
   * not interleaved (2 population with 2 loci): <code>
@@ Line 263: / Line 263: @@
 </code>
+=== SNP data ===
+  * uses the same nucleotide nomenclature as the sequence data
+  * same format as sequence data
+  * linked SNP: more than one site on one line
+  * unlinked SNP: one site per line
+  * two formats:
+    * ''N'': nucleotide format <code>
+N 2 2 Make believe data set using simulated data (2 population and 2 loci)
+4
+3 pop1
+ind1      A
+ind2      A
+ind3      A
+ind1      ACAC
+ind2      ACAC
+ind3      ACGC
+pop2
+ind4      C
+ind5      C
+ind4      TGGA
+ind5      TCGA
+</code>
+    * ''H'': HapMap format <code>
+# using the HapMap data format, but does produce the same result (yet) as the dataset above
+H 2 2 Make believe data set using simulated data (2 population and 2 loci)
+pop1
+    A 3 C 0 3
+A 3 T 0 3
+C 3 G 0 3
+A 2 G 1 3
+C 3 A 0 3
+pop2
+    A 0 C 2 2
+A 0 T 2 2
+C 1 G 1 2
+A 0 G 2 2
+C 0 A 2 2
+</code>
 ===== How to cite =====
 Beerli, P. (2009) How to use migrate or why are markov chain monte carlo programs dicult to use? In G. Bertorelle, M. W. Bruford, H. C. Haue, A. Rizzoli, and C. Vernesi, editors, Population Genetics for Animal Conservation, volume 17 of Conservation Biology, pages 42-79. Cambridge University Press, Cambridge UK, 2009.