+ o The new function mixedFontLabel helps to make labels with bits of
+ text to be plotted in different fonts.
+
+ o There are now replacement operators for [, [[, and $ for the class
+ "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They check
+ that the tip labels are the same in all trees.
+
+ o Objects of class "multiPhylo" can be built with c(): there are
+ methods for the classes "phylo" and "multiPhylo".
+
+ o The internal functions .compressTipLabel and .uncompressTipLabel are
+ now documented.
+
+
+BUG FIXES
+
+ o bind.tree(x, y, where, position = 0) did not work correctly if 'y'
+ was a single-edge tree and 'where' was a tip.
+
+ o rTraitCont() did not use the square-root of branch lengths when
+ simulating a Brownian motion model.
+
+
+
+ CHANGES IN APE VERSION 2.5-2
+
+
+NEW FEATURES
+
+ o There is now a print method for results from ace().
+
+ o There is a labels() method for objects of class "DNAbin".
+
+ o read.dna() has a new option 'as.matrix' to possibly force sequences
+ in a FASTA file to be stored in a matrix (see ?read.dna for details).
+
+
+BUG FIXES
+
+ o as.phylo.hclust() used to multiply edge lengths by 2.
+
+ o A minor bug was fixed in rTraitDisc().
+
+ o ace() sometimes failed (parameter value was NaN and the optimisation
+ failed).
+
+
+DEPRECATED & DEFUNCT
+
+ o evolve.phylo() and plot.ancestral() have been removed.
+
+ o chronogram(), ratogram(), and NPRS.criterion() have been removed.
+
+
+OTHER CHANGES
+
+ o nj() has been improved and is now about 30% faster.
+
+ o The default option 'drop' of [.DNAbin has been changed to FALSE to
+ avoid dropping rownames when selecting a single sequence.
+
+ o print.DNAbin() has been changed to summary.DNAbin() which has been
+ removed.
+
+
+
+ CHANGES IN APE VERSION 2.5-1
+
+
+NEW FEATURES
+
+ o The new function stree generates trees with regular shapes.
+
+ o It is now possible to bind two trees with x + y (see ?bind.tree for
+ details).
+
+ o drop.tip(), extract.clade(), root(), and bind.tree() now have an
+ 'interactive' option to make the operation on a plotted tree.
+
+ o cophyloplot() gains two new arguments 'lwd' and 'lty' for the
+ association links; they are recycled like 'col' (which wasn't before).
+
+
+BUG FIXES
+
+ o rTraitDisc() did not use its 'freq' argument correctly (it was
+ multiplied with the rate matrix column-wise instead of row-wise).
+
+ o [node|tip|edge]labels(thermo = ) used to draw empty thermometers
+ with NA values. Nothing is drawn now like with 'text' or 'pch'.
+ The same bug occurred with the 'pie' option.
+
+ o A bug was fixed in compar.ou() and the help page was clarified.
+
+ o bind.tree() has been rewritten fixing several bugs and making it
+ more efficient.
+
+ o plot.phylo(type = "p") sometimes failed to colour correctly the
+ vertical lines representing the nodes.
+
+ o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches
+ in the correct direction though the tip labels were displayed
+ correctly.
+
+
+OTHER CHANGES
+
+ o The c, cbind, and rbind methods for "DNAbin" objetcs now check that
+ the sequences are correctly stored (in a list for c, in a matrix
+ for the two other functions).
+
+
+
+ CHANGES IN APE VERSION 2.5
+
+
+NEW FEATURES
+
+ o The new function parafit by Pierre Legendre tests for the
+ coevolution between hosts and parasites. It has a companion
+ function, pcoa, that does principal coordinate decomposition.
+ The latter has a biplot method.
+
+ o The new function lmorigin by Pierre Legendre performs multiple
+ regression through the origin with testing by permutation.
+