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--- newhybrids [2011/05/20 13:26] – created heidi
+++ newhybrids [2011/06/03 17:20] (current) – heidi
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 ====== NewHybrids ======
 \\
-**[[http://www2.imm.dtu.dk/~gigu/Geneland/|Geneland]]**\\
+**[[http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm|NewHybrids]]**\\
-[[http://www2.imm.dtu.dk/~gigu/Geneland/Geneland-Doc.pdf|manual]]
+[[http://ib.berkeley.edu/labs/slatkin/eriq/software/new_hybs_doc1_1Beta3.pdf|manual]]
 \\
-NewHybrids (12. April 2011)\\
+NewHybrids version 1.1 beta (7. April 2003)\\
+NewHybrids is a program for computing the posterior distribution that individuals in a sample fall into different hybrid categories.
 \\
-===== Program information =====
+===== Program information =====
+  * Mac
+  * Windows
 \\
 ===== Data type handled =====
+  * diploid
+  * AFLP
+  * MICROSAT
+  * Standard
 \\
 ===== Input Files =====
+  * whitespace (spaces and or tabs) separated text file *.txt/*.dat
+  * first line: ''NumIndivs '' number of individuals
+  * second line: ''NumLoci '' number of loci
+  * third line: ''Digits '' number of digits used to denote a particular allele
+  * fourth line: ''Format '' ''Lumped'' (genotype at a single locus is given by a single number) or ''NonLumped''
+  * next lines: ''LocusNames'' names of all loci separated by whitespace
+  * next lines: genotype data
+    * first character: number of the individual (numbering must be serially)
+    * next characters: genotypes (all on same line or on different lines)
+      * ''Lumped'' format: two alleles are encoded as one number, ''Digits'' specify how many digits are used to represent each locus
+      * ''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'')
 \\
+==== 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
+11 11 11 0 11 32
+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
+123 143 -1 -1 144 144 120 122 157 158 144 144
+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
+11 12 13 11 + + + - +
+22 33 11 22 - - 0 - -
+12 13 13 11 + - - - +
+</code>
 ===== How to cite =====
+Anderson, E.C. and Thompson, E.A. (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160: 1217-1229.