X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fdist.dna.Rd;h=3a5e3e027cb27d599bac0fd9d4b7ba04894e5b93;hb=8de6df204b26f081f2a4c70a500ab97660380692;hp=b2c270a3bf8dfa8845a304f9b924f98912389cdd;hpb=4ceef408de61dc86f0a93b0396aecc6e30cc0d70;p=ape.git

diff --git a/man/dist.dna.Rd b/man/dist.dna.Rd
index b2c270a..3a5e3e0 100644
--- a/man/dist.dna.Rd
+++ b/man/dist.dna.Rd
@@ -109,7 +109,11 @@ 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.}
@@ -139,6 +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.
@@ -176,7 +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}},