transitons and transversions.}
\item{``logdet''}{The Log-Det distance, developed by Lockhart et
- al. (1994), is related to BH87. However, this distance is symmetric.}
+ 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
can be viewed as another variant of the Barry--Hartigan distance.}
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}},