correcting 2 bugs in new dist.gene()

[ape.git] / Changes

diff --git a/Changes b/Changes
index 3d1da0783a81034682838af2c211a3aa44cfbf4e..2fe5b8d492ef56e7adbaa934e1a44a729492b162 100644 (file)
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+++ b/Changes
@@ -1,25 +1,68 @@
+               CHANGES IN APE VERSION 2.2-2
+
+
+NEW FEATURES
+
+    o dist.gene() has been substantially improved and gains an option
+      'pairwise.deletion'.
+
+
+BUG FIXES
+
+    o prop.part() failed with a single tree with the default option
+     'check.labels = TRUE'.
+
+
+
                CHANGES IN APE VERSION 2.2-1
 
 
 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.
+
+    o read.nexus() failed to place correctly tip labels when reading
+      a single tree with no edge lengths.
+
+    o A bug was fixed in sh.test().
+
 
 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