- CHANGES IN APE VERSION 3.0-2
+ CHANGES IN APE VERSION 3.0-5
+
+
+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 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 numerically more accurate.
+
+ o The C code of fastme.*() has been slightly modified and should
+ be more stable by avoiding passing character strings (the
+ results are identical to the previous versions).
+
+ o The file src/newick.c has been removed.
+
+
+
+ CHANGES IN APE VERSION 3.0-3
BUG FIXES
a result is returned in most cases.
+OTHER CHANGES
+
+ o Because of problems with character string manipulation in C, the
+ examples in ?bionj and in ?fastme have been disallowed. In the
+ meantime, these functions might be unstable. This will be solved
+ for the next release.
+
+
CHANGES IN APE VERSION 3.0-2
projects / ape.git / blobdiff