- CHANGES IN APE VERSION 2.5-1
+ CHANGES IN APE VERSION 2.5-2
+
+
+NEW FEATURES
+
+ o There is now a print method for results from ace().
+
+
+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.
+
+
+
+ CHANGES IN APE VERSION 2.5-1
NEW FEATURES
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 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