various corrections

[ape.git] / Changes

diff --git a/Changes b/Changes
index e63867fd5d815263850cedd7f7fd02228b1e2c0e..86d013187c44865657ece0081afa18c55ee5401a 100644 (file)
--- a/Changes
+++ b/Changes
@@ -3,14 +3,32 @@
 
 NEW FEATURES
 
+    o The new function makeLabel() helps to modify labels of trees,
+      lists of trees, or DNA sequences, with several utilities to
+      truncate and/or make them unique, substituting some
+      characters, and so on.
+
     o The new function del.gaps() removes insertion gaps ("-") in a
       set of DNA sequences.
 
+    o read.dna() can now read Clustal files (*.aln).
+
 
 BUG FIXES
 
-    o root() failed with resolve.root = TRUE when the root was already
-      the specified root.
+    o root() failed with 'resolve.root = TRUE' when the root was
+      already the specified root.
+
+    o Several bugs were fixed in mlphylo().
+
+    o collapsed.singles() did not propagate the 'Nnode' and
+      'node.labels' elements (thanks to Elizabeth Purdom for the fix).
+
+    o read.nexus() failed to remove correctly the comments within
+      trees.
+
+    o read.nexus() failed to read a file with a single tree and no
+      translation of tip labels.
 
 
 OTHER CHANGES
@@ -18,6 +36,12 @@ OTHER CHANGES
     o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
       Minin.
 
+    o The option 'check.labels' of consensus() and prop.part() is now
+      TRUE by default.
+
+    o write.dna() now does not truncate names to 10 characters with
+      the Phylip formats.
+
 
 
                CHANGES IN APE VERSION 2.2