One way to organize the data is by markers. For each marker, you give the genotypes of the individuals. The order of the individuals has to be the same for each marker. Below is an example. After the -start markers, the program expects a repeating sequence of marker name, then n marker genotypes where n is the sample size. The marker names should match those in the Map file.
-start markers Marker1_1 2 2 2 2 2 1 1 1 1 1 Marker1_2 2 2 2 1 1 1 1 1 1 1 Marker1_3 1 2 2 2 2 1 1 1 1 1 Marker1_4 1 1 2 2 2 1 1 1 1 1 Marker1_5 2 2 2 2 2 1 1 1 1 1 Marker2_1 2 1 1 2 2 1 1 1 1 1 Marker2_2 2 2 2 1 1 1 1 1 1 1 Marker2_3 2 2 1 1 1 1 2 2 2 2 Marker2_4 2 1 1 1 1 1 1 1 2 2 -stop markers
The traits are encoded in the same fashion. After the -start traits
tokens, the program expects a repeating sequence of trait name and then
n values for the sample.
The order of the individuals has to be the same as in the markers. Also,
you can specify the token for a missing trait with
-missingtrait .
If you want a lone period to indicate a missing datum.
-start traits Trait_1 5.0 5.3 6.2 4.1 5.5 5.8 6.7 6.1 . 6.4 Trait_2 15.0 15.3 16.2 24.1 25.5 25.8 16.7 26.1 33.2 16.4 -stop traits ... indicates the end of the trait data.
Categorical (otraits) are other traits that will be stored as character strings. These will be things such as sex, brood, eye color, etc. Each token should be less than 64 characters in length. The -missingtrait token can be reused with a different token if desired.
-start otraits Sex M F M M M F F M F F Brood 1 1 1 1 1 2 2 2 2 2 -stop otraits