Dear all,
The version 1.0 of ape (analysis of phylogenetics and evolution) is now on
CRAN. The jump from version 0.2-1 to 1.0 is explained by the fact that the
initial objectives of the project have been completed. The relevant part of
the Changes file is shown below. All comments, suggestions, or bug reports
are welcome.
Emmanuel Paradis
CHANGES IN APE VERSION 1.0
NEW FEATURES
o Two new functions, read.dna() and write.dna(), read/write in a file
DNA sequences in interleaved or in sequential format.
o Two new functions, read.nexus() and write.nexus(), read/write trees
in a NEXUS file.
o The new function bind.tree() allows to bind two trees together,
possibly handling root edges to give internal branches.
o The new function drop.tip() removes the tips in a phylogenetic tree,
and trims (or not) the corresponding internal branches.
o The new function is.ultrametric() tests if a tree is ultrametric.
o The function plot.phylo() has more functionalities such as drawing the
branches with different colours and/or different widths, showing the
node labels, controling the position and font of the labels, rotating
the labels, and controling the space around the plot.
o The function read.tree() can now read trees with no branch length,
such as "(a,b),c);". Consequently, the element
`edge.length' in
objects of class "phylo" is now optional.
o The function write.tree() has a new default behaviour: if the default
for the option `file' is used (i.e. file = ""), then a
variable of
mode character containing the tree in Newick format is returned which
can thus be assigned (e.g., tree <- write.tree(phy)).
o The function read.tree() has a new argument `text' which allows
to read the tree in a variable of mode character.
o A new data set is included: the phylogenetic relationships among
the orders of birds from Sibley and Ahlquist (1990).
