		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).



		CHANGES IN APE VERSION 0.2-1


BUG FIXES

    o Several bugs were fixed in the help pages.



		CHANGES IN APE VERSION 0.2


NEW FEATURES

    o The function write.tree() writes phylogenetic trees (objects of class
      "phylo") in an ASCII file using the Newick parenthetic format.

    o The function birthdeath() fits a birth-death model to branching times
      by maximum likelihood, and estimates the corresponding speciation and
      extinction rates.

    o The function scale.bar() adds a scale bar to a plot of a phylogenetic
      tree.

    o The function is.binary.tree() tests whether a phylogeny is binary.

    o Two generic functions, coalescent.intervals() and collapsed.intervals(),
      as well as some methods are introduced.

    o Several functions, including some generics and methods, for computing
      skyline plot estimates (classic and generalized) of effective
      population size through time are introduced and replace the function
      skyline.plot() in version 0.1.

    o Two data sets are now included: the phylogenetic relationships among
      the families of birds from Sibley and Ahlquist (1990), and an
      estimated clock-like phylogeny of HIV sequences sampled in the
      Democratic Republic of Congo.


DEPRECATED & DEFUNCT

    o The function skyline.plot() in ape 0.1 has been deprecated and
      replaced by more elaborate functions (see above).


BUG FIXES

    o Two important bugs were fixed in plot.phylo(): phylogenies with
      multichotomies not at the root or not with only terminal branches,
      and phylogenies with a single node (i.e. only terminal branches)
      did not plot. These trees should be plotted correctly now.

    o Several bugs were fixed in diversi.time() in the computation of
      AICs and LRTs.

    o Various errors were corrected in the help pages.
