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 failed. (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 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