+ CHANGES IN APE VERSION 3.0-6
+
+
+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
BUG FIXES
- o read.dna() failed to read interleaved files if the first line
- uses tabulations instead of white spaces.
+ o read.dna() failed to read Phylip files if the first line used
+ tabulations instead of white spaces.
+
+ o read.dna() failed to read Phylip or Clustal files with less than
+ 10 nucleotides. (See other changes in this function below.)
OTHER CHANGES
+ o read.dna() now requires at least one space (or tab) between the
+ 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.
o The C code of bionj() has been reworked: it is more stable (by
avoiding passing character strings), slightly faster (by about
- 20%), and more accurate numerically.
+ 20%), and numerically more accurate.
o The C code of fastme.*() has been slightly modified and should
be more stable by avoiding passing character strings (the