This function gives the indices of segregating (polymorphic) sites in a sample of DNA sequences.
seg.sites(x, strict = FALSE, trailingGapsAsN = TRUE)
a matrix or a list which contains the DNA sequences.
a logical value; if TRUE
, ambiguities and gaps in
the sequences are not interpreted in the usual way.
a logical value; if TRUE
(the default),
the leading and trailing alignment gaps are considered as unknown
bases (i.e., N).
A numeric (integer) vector giving the indices of the segregating sites.
If the sequences are in a list, they must all be of the same length.
If strict = FALSE
(the default), the following rule is used to
determine if a site is polymorphic or not in the presence of ambiguous
bases: `A' and `R' are not interpreted as different, `A' and `Y' are
interpreted as different, and `N' and any other base (ambiguous or
not) are interpreted as not different. If strict = TRUE
, all
letters are considered different.
Alignment gaps are considered different from all letters except for
the leading and trailing gaps if trailingGapsAsN = TRUE
(which
is the default).
base.freq
, theta.s
, nuc.div
(last two in pegas)
# NOT RUN {
data(woodmouse)
y <- seg.sites(woodmouse)
y
length(y)
# }
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