bug corrected in del.gaps + small change in man page of theta.s

[ape.git] / Changes

diff --git a/Changes b/Changes
index 4aa9a918f92a3056f6a3ee439cd2b64a76f2042c..854ae1949d3b84ed1ca5e8ade91a4cf660ef94a2 100644 (file)
--- a/Changes
+++ b/Changes
@@ -1,11 +1,85 @@
+               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'.
+
+   o summary.DNAbin() failed to display correctly the summary of
+     sequence lengths with lists of sequences of 10,000 bases or more
+     (because summary.default uses 4 significant digits by default).
+
+   o read.nexus() failed to read a file with a single tree with line
+     breaks in the Newick string.
+
+   o del.gaps() returned a list of empty sequences when there were no
+     gaps.
+
+
+OTHER CHANGES
+
+    o The data sets bird.orders and bird.families are now stored as
+      Newick strings; i.e., the command data(bird.orders) calls
+      read.tree().
+
+
+
                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 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
@@ -184,9 +258,9 @@ BUG FIXES
 
 OTHER CHANGES
 
-    o The code of mlphylo() has almost entirely rewritten, and should
-      be much stabler. The options have been also greatly simplified
-      (see ?mlphylo and ?DNAmodel for details).
+    o The code of mlphylo() has been almost entirely rewritten, and
+      should be much stabler. The options have been also greatly
+      simplified (see ?mlphylo and ?DNAmodel for details).
 
     o The internal function nTips has been renamed klastorin_nTips.