+ CHANGES IN APE VERSION 2.3
+
+
+NEW FEATURES
+
+ o The new functions CADM.global and CADM.post, contributed by
+ Pierre Legendre, test the congruence among several distance
+ matrices.
+
+ o The new function yule.time fits a user-defined time-dependent
+ Yule model by maximum likelihood.
+
+ o The new function makeNodeLabel creates and/or modifies node
+ labels in a flexible way.
+
+ o read.tree() and write.tree() have been modified so that they can
+ handle individual tree names.
+
+ o plot.phylo() has a new argument 'edge.lty' that specifies the
+ types of lines used for the edges (plain, dotted, dashed, ...)
+
+ o phymltest() has been updated to work with PhyML 3.0.1.
+
+
+BUG FIXES
+
+ o drop.tip() shuffled tip labels in some cases.
+
+ o drop.tip() did not handle node.label correctly.
+
+ o is.ultrametric() now checks the ordering of the edge matrix.
+
+ o ace() sometimes returned negative values of likelihoods of
+ ancestral states (thanks to Dan Rabosky for solving this long
+ lasting bug).
+
+
+OTHER CHANGES
+
+ o The data set xenarthra has been removed.
+
+
+
+ CHANGES IN APE VERSION 2.2-4
+
+BUG FIXES
+
+ o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
+ now fixed. (Thanks to Peter Wragg for the fix!)
+
+ o A warning message occurred for no reason with ace(method="GLS").
+
+
+OTHER CHANGES
+
+ o There is now a general help page displayed with '?ape'
+
+
+
+ CHANGES IN APE VERSION 2.2-3
+
+
+NEW FEATURES
+
+ o The new function extract.clade extracts a clade from a tree by
+ specifying a node number or label.
+
+ o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
+ operations of the same names.
+
+ o dist.dna() can now return the number of site differences by
+ specifying model="N".
+
+
+BUG FIXES
+
+ o chronopl() did not work with CV = TRUE.
+
+ o read.nexus() did not work correctly in some situations (trees on
+ multiple lines with different numbers of lines and/or with
+ comments inserted within the trees).
+
+ o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
+ the number of lineages with non-binary trees.
+
+
+OTHER CHANGES
+
+ o ape has now a namespace.
+
+ o drip.tip() has been improved: it should be much faster and work
+ better in some cases (e.g., see the example in ?zoom).
+
+
+
CHANGES IN APE VERSION 2.2-2