CHANGES IN APE VERSION 1.1-2


NEW FEATURES

    o The Tamura and Nei (1993) model of DNA distance is now implemented
      in dist.dna(): five models are now available in this function.

    o A new data set is included: a set of 15 sequences of the
      cytochrome b mitochondrial gene of the woodmouse (Apodemus
      sylvaticus).


BUG FIXES

    o A bug in read.nexus() was fixed.

    o read.dna() previously did not work correctly in most cases.
      The function has been completely re-written and its help page
      has been considerably extended (see ?read.dna for details).
      Underscores (_) in taxon names are no more replaced with
      spaces (this behaviour was undocumented).

    o A bug was fixed in write.dna().



		CHANGES IN APE VERSION 1.1-1


BUG FIXES

    o A bug in read.tree() introduced in APE 1.1 was fixed.

    o A bug in compar.gee() resulted in an error when trying to fit
      a model with `family = "binomial"'. This is now fixed.



 		CHANGES IN APE VERSION 1.1


NEW FEATURES

    o The Klastorin (1982) method as suggested by Misawa and Tajima
      (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
      on the basis of phylogenetic trees has been implemented (see
      the function klastorin()). 

    o Functions have been added to convert APE's "phylo" objects in
      "hclust" cluster objects and vice versa (see the help page of
      as.phylo for details).

    o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
      are introduced for the estimation of absolute evolutionary rates
      (ratogram) and dated clock-like trees (chronogram) from
      phylogenetic trees using the non-parametric rate smoothing approach
      by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).

    o A summary method is now provided printing a summary information on a
      phylogenetic tree with, for instance, `summary(tree)'.

    o The behaviour of read.tree() was changed so that all spaces and
      tabulations in tree files are now ignored. Consequently, spaces in tip
      labels are no more allowed. Another side effect is that read.nexus()
      now does not replace the underscores (_) in tip labels with spaces
      (this behaviour was undocumented).
      
    o The function plot.phylo() has a new option (`underscore') which
      specifies whether the underscores in tip labels should be written on
      the plot as such or replaced with spaces (the default).

    o The function birthdeath() now computes 95 % confidence intervals of
      the estimated parameters using profile likelihood.
      
    o Three new data sets are included: a gene tree estimated from 36
      landplant rbcL sequences, a gene tree estimated from 32 opsin
      sequences, and a gene tree for 50 BRCA1 mammalian sequences.


BUG FIXES
      
    o A bug was fixed in dist.gene() where nothing was returned.

    o A bug in plot.mst() was fixed.

    o A bug in vcv.phylo() resulted in false correlations when the
      option `cor = TRUE' was used (now fixed).



		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.