NEW FEATURES
+ o The new function chronos estimates chronograms by penalised
+ likelihood and maximum likelihood with a completely reworked
+ code and interface. There is a new function makeChronosCalib to
+ set the calibration points easily. chronos() will eventually
+ replace chronopl().
+
+ o The new function 'where' searches patterns in DNA sequences.
+
o pic() gains an option 'rescaled.tree = FALSE' to return the tree
- with its branch lengths rescaled for the PICs calculation.
+ with its branch lengths rescaled for the PIC calculation.
+
+ o clustal(), muscle(), and tcoffee() gain an option
+ 'original.ordering = TRUE' to ease the comparisons of
+ alignments.
+
+ o plot.phylo() has a new option, open.angle, used when plotting
+ circular trees.
+
+ o The new function read.FASTA reads FASTA files much faster and
+ more efficiently. It is called internally by read.dna(, "fasta")
+ or can be called directly.
BUG FIXES
o drop.tip() shuffled node labels on some trees.
+ o axisPhylo() now works correctly with circular trees, and gives a
+ sensible error message when type = "r" or "u".
+
+
+OTHER CHANGES
+
+ o .compressTipLabel() is 10 times faster thanks to Joseph Brown.
+
+ o base.freq() is now faster with lists.
+
+ o as.matrix.DNAbin() should be faster and more efficient with
+ lists; it now accepts vectors.
+
+ o collapse.singles() is faster thanks to Klaus Schliep. This will
+ speed-up drop.tip() significantly.
+
CHANGES IN APE VERSION 3.0-6
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
+ o write.nexus() now writes tree names in the NEXUS file if given a
list of trees with names.