+ CHANGES IN APE VERSION 2.6-4
+
+
+NEW FEATURES
+
+ o There is a new image() method for "DNAbin" objects: it plots DNA
+ alignments in a flexible and efficient way.
+
+ o Two new functions as.network.phylo and as.igraph.phylo convert
+ trees of class "phylo" into these respective network classes
+ defined in the packages of the same names.
+
+ o The three new functions clustal, muscle, and tcoffee perform
+ nucleotide sequence alignment by calling the external programs
+ of the same names.
+
+ o base.freq() gains an option 'all' to count all the possible bases
+ including the ambiguous ones (defaults to FALSE).
+
+ o read.nexus() now writes tree names in the NEXUS file if given a
+ list of trees with names.
+
+
+BUG FIXES
+
+ o prop.part() failed in some situations with unrooted trees.
+
+ o read.nexus() shuffled node labels when a TRANSLATE block was
+ present.
+
+ o varCompPhylip() did not work if 'exec' was specified.
+
+ o bind.tree() shuffled node labels when position > 0 and 'where'
+ was not the root.
+
+
+OTHER CHANGES
+
+ o BaseProportion in src/dist_dna.c has been modified.
+
+ o A number of functions in src/tree_build.c have been modified.
+
+ o The matching representation has now only two columns as the third
+ column was redundant.
+
+
+
+ CHANGES IN APE VERSION 2.6-3
+
+
+NEW FEATURES
+
+ o rTraitCont() and rTraitDisc() gains a '...' argument used with
+ user-defined models (suggestion by Gene Hunt).
+
+
+BUG FIXES
+
+ o as.hclust.phylo() now returns an error with unrooted trees.
+
+ o as.hclust.phylo() failed with trees with node labels (thanks to
+ Jinlong Zhang for pointing this bug out).
+
+ o read.dna(, "fasta") failed if sequences were not all of the same
+ length.
+
+ o plot.phylo() did not recycle values of 'font', 'cex' and
+ 'tip.color' correctly when type = "fan" or "radial".
+
+ o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
+ "unrooted" with lab4ut = "axial" (the placement of tip labels still
+ needs to be improved with lab4ut = "horizontal").
+
+
+OTHER CHANGES
+
+ o In drop.fossil() the default tol = 0 has been raised to 1e-8.
+
+ o The help command ?phylo now points to the man page of read.tree()
+ where this class is described. Similarly, ?matching points to the
+ man page of as.matching().
+
+
+