Find Segregating Sites in DNA Sequences
This function gives the indices of segregating (polymorphic) sites in a sample of DNA sequences.
- a matrix or a list which contains the DNA sequences.
If the sequences are in a list, all the sequences must be of the same length. Ambiguous nucleotides are ignored.
- A numeric (integer) vector giving the indices of the segregating sites.
The present version looks for the sites which are ``variable'' in the data in terms of different letters. This may give unexpected results if there are ambiguous bases in the data.
data(woodmouse) y <- seg.sites(woodmouse) y length(y)