base.freq = NULL, as.matrix = FALSE)
}
\arguments{
- \item{x}{a matrix or a list containing the DNA sequences.}
- \item{model}{a character string specifying the evlutionary model to be
- used; must be one of \code{"raw"}, \code{"N"}, \code{"JC69"},
- \code{"K80"} (the default), \code{"F81"}, \code{"K81"},
- \code{"F84"}, \code{"BH87"}, \code{"T92"}, \code{"TN93"},
- \code{"GG95"}, \code{"logdet"}, or \code{"paralin"}.}
+ \item{x}{a matrix or a list containing the DNA sequences; this must be
+ of class \code{"DNAbin"} (use \code{\link{as.DNAbin}} is they are
+ stored as character).}
+ \item{model}{a character string specifying the evolutionary model to be
+ used; must be one of \code{"raw"}, \code{"N"}, \code{"TS"},
+ \code{"TV"}, \code{"JC69"}, \code{"K80"} (the default),
+ \code{"F81"}, \code{"K81"}, \code{"F84"}, \code{"BH87"},
+ \code{"T92"}, \code{"TN93"}, \code{"GG95"}, \code{"logdet"},
+ \code{"paralin"}, \code{"indel"}, or \code{"indelblock"}.}
\item{variance}{a logical indicating whether to compute the variances
of the distances; defaults to \code{FALSE} so the variances are not
computed.}
- \item{gamma}{a value for the gamma parameter which is possibly used to
- apply a gamma correction to the distances (by default \code{gamma =
- FALSE} so no correction is applied).}
+ \item{gamma}{a value for the gamma parameter possibly used to apply a
+ correction to the distances (by default no correction is applied).}
\item{pairwise.deletion}{a logical indicating whether to delete the
sites with missing data in a pairwise way. The default is to delete
- the sites with at least one missing data for all sequences.}
+ the sites with at least one missing data for all sequences (ignored
+ if \code{model = "indel"} or \code{"indelblock"}).}
\item{base.freq}{the base frequencies to be used in the computations
- (if applicable, i.e. if \code{method = "F84"}). By default, the
- base frequencies are computed from the whole sample of sequences.}
+ (if applicable). By default, the base frequencies are computed from
+ the whole set of sequences.}
\item{as.matrix}{a logical indicating whether to return the results as
a matrix. The default is to return an object of class
\link[stats]{dist}.}
brief description is given below; more details can be found in the
References.
- \item{``raw'', ``N''}{This is simply the proportion or the number of
+\itemize{
+ \item{\code{raw}, \code{N}: }{This is simply the proportion or the number of
sites that differ between each pair of sequences. This may be useful
to draw ``saturation plots''. The options \code{variance} and
\code{gamma} have no effect, but \code{pairwise.deletion} can.}
- \item{``JC69''}{This model was developed by Jukes and Cantor (1969). It
+ \item{\code{TS}, \code{TV}: }{These are the numbers of transitions and
+ transversions, respectively.}
+
+ \item{\code{JC69}: }{This model was developed by Jukes and Cantor (1969). It
assumes that all substitutions (i.e. a change of a base by another
one) have the same probability. This probability is the same for all
sites along the DNA sequence. This last assumption can be relaxed by
default, no gamma correction is applied. Another assumption is that
the base frequencies are balanced and thus equal to 0.25.}
- \item{``K80''}{The distance derived by Kimura (1980), sometimes referred
+ \item{\code{K80}: }{The distance derived by Kimura (1980), sometimes referred
to as ``Kimura's 2-parameters distance'', has the same underlying
assumptions than the Jukes--Cantor distance except that two kinds of
substitutions are considered: transitions (A <-> G, C <-> T), and
Jukes--Cantor model, the gamma parameter must be given by the
user. By default, no gamma correction is applied.}
- \item{``F81''}{Felsenstein (1981) generalized the Jukes--Cantor model
+ \item{\code{F81}: }{Felsenstein (1981) generalized the Jukes--Cantor model
by relaxing the assumption of equal base frequencies. The formulae
used in this function were taken from McGuire et al. (1999)}.
- \item{``K81''}{Kimura (1981) generalized his model (Kimura 1980) by
+ \item{\code{K81}: }{Kimura (1981) generalized his model (Kimura 1980) by
assuming different rates for two kinds of transversions: A <-> C and
G <-> T on one side, and A <-> T and C <-> G on the other. This is
what Kimura called his ``three substitution types model'' (3ST), and
is sometimes referred to as ``Kimura's 3-parameters distance''}.
- \item{``F84''}{This model generalizes K80 by relaxing the assumption
+ \item{\code{F84}: }{This model generalizes K80 by relaxing the assumption
of equal base frequencies. It was first introduced by Felsenstein in
1984 in Phylip, and is fully described by Felsenstein and Churchill
(1996). The formulae used in this function were taken from McGuire
et al. (1999)}.
- \item{``BH87''}{Barry and Hartigan (1987) developed a distance based
+ \item{\code{BH87}: }{Barry and Hartigan (1987) developed a distance based
on the observed proportions of changes among the four bases. This
distance is not symmetric.}
- \item{``T92''}{Tamura (1992) generalized the Kimura model by relaxing
+ \item{\code{T92}: }{Tamura (1992) generalized the Kimura model by relaxing
the assumption of equal base frequencies. This is done by taking
into account the bias in G+C content in the sequences. The
substitution rates are assumed to be the same for all sites along
the DNA sequence.}
- \item{``TN93''}{Tamura and Nei (1993) developed a model which assumes
+ \item{\code{TN93}: }{Tamura and Nei (1993) developed a model which assumes
distinct rates for both kinds of transition (A <-> G versus C <->
T), and transversions. The base frequencies are not assumed to be
equal and are estimated from the data. A gamma correction of the
inter-site variation in substitution rates is possible.}
- \item{``GG95''}{Galtier and Gouy (1995) introduced a model where the
+ \item{\code{GG95}: }{Galtier and Gouy (1995) introduced a model where the
G+C content may change through time. Different rates are assumed for
transitons and transversions.}
- \item{``logdet''}{The Log-Det distance, developed by Lockhart et
- al. (1994), is related to BH87. However, this distance is symmetric.}
+ \item{\code{logdet}: }{The Log-Det distance, developed by Lockhart et
+ al. (1994), is related to BH87. However, this distance is
+ symmetric. Formulae from Gu and Li (1996) are used.
+ \code{dist.logdet} in \pkg{phangorn} uses a different
+ implementation that gives substantially different distances for
+ low-diverging sequences.}
- \item{``paralin''}{Lake (1994) developed the paralinear distance which
+ \item{\code{paralin}: }{Lake (1994) developed the paralinear distance which
can be viewed as another variant of the Barry--Hartigan distance.}
-}
+
+ \item{\code{indel}: }{this counts the number of sites where there is an
+ insertion/deletion gap in one sequence and not in the other.}
+
+ \item{\code{indelblock}: }{same than before but contiguous gaps are
+ counted as a single unit. Note that the distance between \code{-A-} and
+ \code{A--} is 3 because there are three different blocks of gaps, whereas
+ the ``indel'' distance will be 2.}
+}}
\value{
an object of class \link[stats]{dist} (by default), or a numeric
matrix if \code{as.matrix = TRUE}. If \code{model = "BH87"}, a numeric
sequences of unequal base compositions. \emph{Proceedings of the
National Academy of Sciences USA}, \bold{92}, 11317--11321.
+ Gu, X. and Li, W.-H. (1996) Bias-corrected paralinear and LogDet
+ distances and tests of molecular clocks and phylogenies under
+ nonstationary nucleotide frequencies. \emph{Molecular Biology and
+ Evolution}, \bold{13}, 1375--1383.
+
Jukes, T. H. and Cantor, C. R. (1969) Evolution of protein
molecules. in \emph{Mammalian Protein Metabolism}, ed. Munro, H. N.,
pp. 21--132, New York: Academic Press.
substitutions in the control region of mitochondrial DNA in humans and
chimpanzees. \emph{Molecular Biology and Evolution}, \bold{10}, 512--526.
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\seealso{
\code{\link{read.GenBank}}, \code{\link{read.dna}},
\code{\link{write.dna}}, \code{\link{DNAbin}},
projects / ape.git / blobdiff