seg.sites {ape} | R Documentation |
This function gives the indices of segregating (polymorphic) sites in a sample of DNA sequences.
seg.sites(x)
x |
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.
Emmanuel Paradis
base.freq
, GC.content
,
theta.s
, nuc.div
data(woodmouse) y <- seg.sites(woodmouse) y length(y)