+ CHANGES IN APE VERSION 2.1-2
+
+
+NEW FEATURES
+
+ o There three new methods for the "multiPhylo" class: str, $,
+ and [[.
+
+ o root() gains the options 'node' and 'resolve.root'
+ (FALSE by default) as well as its code being improved.
+
+ o mltt.plot() has now an option 'log' used in the same way
+ than in plot.default().
+
+
+BUG FIXES
+
+ o mltt.plot() failed to display the legend with an unnamed
+ list of trees.
+
+ o nodelabels() with pies now correcly uses the argument
+ 'cex' to draw symbols of different sizes (which has
+ worked already for thermometers).
+
+ o read.nexus() generally failed to read very big files.
+
+
+OTHER CHANGES
+
+ o The argument 'family' of compar.gee() can now be a function
+ as well as a character string.
+
+ o read.tree() and read.nexus() now return an unnamed list if
+ 'tree.names = NULL'.
+
+ o read.nexus() now returns a modified object of class "multiPhylo"
+ when there is a TRANSLATE block in the NEXUS file: the individual
+ trees have no 'tip.label' vector, but the list has a 'TipLabel'
+ attribute. The new methods '$' and '[[' set these elements
+ correctly when extracting trees.
+
+
+
CHANGES IN APE VERSION 2.1-1
o The new function rmtree generates lists of random trees.
+ o rcoal() now generates a genuine coalescent tree by default
+ (thanks to Vladimir Minin for the code).
+
+
+BUG FIXES
+
+ o nuc.div() returned an incorrect value with the default
+ pairwise.deletion = FALSE.
+
+
+OTHER CHANGES
+
+ o The internal codes of bionj(), fastme.bal(), and fastme.ols()
+ have been improved so that they are stabler and faster.
+
+ o R packages used by ape are now loaded silently; lattice and gee
+ are loaded only when needed.
+
CHANGES IN APE VERSION 2.1