provisional version of the new reorder.phylo()

[ape.git] / NEWS

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+               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
 
 
 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