new speciesTree()

[ape.git] / man / dist.dna.Rd

diff --git a/man/dist.dna.Rd b/man/dist.dna.Rd
index d5857e2e05a85f8d71d9cf773b795c9ea2aa5271..3a5e3e027cb27d599bac0fd9d4b7ba04894e5b93 100644 (file)
--- a/man/dist.dna.Rd
+++ b/man/dist.dna.Rd
@@ -7,12 +7,14 @@ dist.dna(x, model = "K80", variance = FALSE,
          base.freq = NULL, as.matrix = FALSE)
 }
 \arguments{
-  \item{x}{a matrix or a list containing the DNA sequences.}
+  \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 evlutionary model to be
-    used; must be one of \code{"raw"}, \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"}.}
+    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{variance}{a logical indicating whether to compute the variances
     of the distances; defaults to \code{FALSE} so the variances are not
     computed.}
@@ -40,10 +42,11 @@ dist.dna(x, model = "K80", variance = FALSE,
   brief description is given below; more details can be found in the
   References.
 
-  \item{``raw''}{This is simply the proportion 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.}
+\itemize{
+  \item{``raw'', ``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
     assumes that all substitutions (i.e. a change of a base by another
@@ -106,11 +109,15 @@ dist.dna(x, model = "K80", variance = FALSE,
     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.}
-}
+}}
 \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
@@ -136,6 +143,11 @@ dist.dna(x, model = "K80", variance = FALSE,
   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.
@@ -173,7 +185,7 @@ dist.dna(x, model = "K80", variance = FALSE,
   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}},