Usage
dist.dna(x, y = NULL, variance = FALSE, gamma = NULL,
method = "Kimura", basefreq = NULL, GCcontent = NULL)
dist.dna.JukesCantor(x, y, variance = FALSE, gamma = NULL)
dist.dna.TajimaNei(x, y, variance = FALSE, basefreq = NULL)
dist.dna.Kimura(x, y, variance = FALSE, gamma = NULL)
dist.dna.Tamura(x, y, variance = FALSE, GCcontent = NULL)
Arguments
x
either, a vector with a single DNA sequence, or a matrix of
DNA sequences, or a list of DNA sequences (the latter can be taken
from, e.g., read.GenBank
).
y
a vector with a single DNA sequence.
gamma
a value for the gamma parameter which is possibly used to
apply a gamma correction to the distances (by default gamma =
NULL
so no correction is applied).
variance
a logical indicating whether to compute the variances
of the distances; defaults to FALSE
so the variances are not
computed.
method
a character string specifying the method used to compute
the distance. Currently four choices are possible: "JukesCantor"
,
"TajimaNei"
, "Kimura"
(the default), and "Tamura"
.
basefreq
the base frequencies to be used in the computations
(if applicable, i.e. if method = "TajimaNei"
). By default, the
base frequencies are computed from the whole sample of sequences.
GCcontent
the content in G+C to be used in the computations
(if applicable, i.e. if method = "Tamura"
). By default, this
percentage is computed from the whole sample of sequences.