+ CHANGES IN APE VERSION 3.0-8
+
+
+NEW FEATURES
+
+ o ace() gains a new option 'use.expm' to use expm() from the
+ package of the same name in place of matexpo().
+
+
+BUG FIXES
+
+ o read.dna(, "fasta") may add '\r' in labels: this is fixed.
+
+ o prop.clades() returned wrong numbers when the tip labels of
+ 'phy' are not in the same order than the list of trees (thanks
+ to Rupert Collins for the report).
+
+ o CADM.post() displayed "1" on the diagonal of the matrix of
+ Mantel p-values. It now displays "NA" on the diagonal,
+ indicating that no test of significance is computed between a
+ distance matrix and itself.
+
+
+
CHANGES IN APE VERSION 3.0-7
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.
+
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.