[R] ape 1.0 is on CRAN

Emmanuel Paradis paradis at isem.univ-montp2.fr
Mon Mar 10 19:02:56 CET 2003

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



     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).

More information about the R-help mailing list