X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=ec8918ae97f2c4e7d9bfe7e8a7d19fc2a6599041;hb=199144b0297c3fc76d76c29e561151235e39f0af;hp=3660ac41656c766a522d731a10cfc489ae01c384;hpb=477a8f1b7e5841202ef29d3d8af3c93acd35c043;p=ape.git

diff --git a/NEWS b/NEWS
index 3660ac4..ec8918a 100644
--- a/NEWS
+++ b/NEWS
@@ -1,4 +1,51 @@
-		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
@@ -7,6 +54,14 @@ 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