+ CHANGES IN APE VERSION 3.0-6
+
+
+NEW FEATURES
+
+ o reorder.phylo() has a new order, "postorder", and a new option
+ index.only = TRUE to return only the vector of indices (the tree
+ is unmodified; see ?reorder.phylo for details).
+
+
+BUG FIXES
+
+ o reorder(, "pruningwise") made R crash if the rows of the edge
+ matrix are in random order.
+
+
+OTHER CHANGES
+
+ o dist.nodes() is now 6 to 10 times faster.
+
+ o reorder(, "cladewise") is now faster. The change is not very
+ visible for small trees (n < 1000) but this can be more than
+ 1000 faster for big trees (n >= 1e4).
+
+
+
+ CHANGES IN APE VERSION 3.0-5
+
+
+BUG FIXES
+
+ o ace() should better catch errors when SEs cannot be computed.
+
+
+OTHER CHANGES
+
+ o write.dna(format = "fasta") now conforms more closely to the
+ FASTA standard thanks to François Michonneau.
+
+ o print.DNAbin() does not print base compositions if there are more
+ than one million nucleotides.
+
+
+
CHANGES IN APE VERSION 3.0-4
tabulations instead of white spaces.
o read.dna() failed to read Phylip or Clustal files with less than
- 10 nucleotides failed. (See other changes in this function
- below.)
+ 10 nucleotides. (See other changes in this function below.)
OTHER CHANGES
taxa names and the sequences (whatever the length of taxa
names). write.dna() now follows the same rule.
+ o The option 'seq.names' of read.dna has been removed.
+
o The files ape-defunct.R and ape-defunct.Rd, which have not been
modified for almost two years, have been removed.