various corrections

[ape.git] / Changes

diff --git a/Changes b/Changes
index 19e350a2dbedeb0bffbc50a9ac0eb2fb17394c58..86d013187c44865657ece0081afa18c55ee5401a 100644 (file)
--- a/Changes
+++ b/Changes
@@ -1,4 +1,70 @@
-               CHANGES IN APE VERSION 2.1-4
+               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.
+
+
+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
+
+
+NEW FEATURES
+
+    o Four new functions have been written by Damien de Vienne for the
+      graphical exploration of large trees (cophyloplot, subtrees,
+      subtreeplot), and to return the graphical coordinates of tree
+      (without plotting).
+
+    o The new functions corPagel and corBlomberg implement the Pagel's
+      "lambda" and Blomberg et al.'s "ACDC" correlation structures.
+
+    o chronopl() has been improved and gains several options: see its
+      help page for details.
+
+    o boot.phylo() has now an option 'trees' to possibly return the
+      bootstraped trees (the default is FALSE).
+
+    o prop.part() has been improved and should now be faster in all
+      situations.
 
 
 BUG FIXES
@@ -12,11 +78,15 @@ BUG FIXES
     o Drawing the tip labels sometimes failed when plotting circular
       trees.
 
+    o zoom() failed when tip labels were used instead of their numbers
+      (thanks to Yan Wong for the fix).
 
-OTHER CHANGES
+    o drop.tip() failed with some trees (fixed by Yan Wong).
 
-    o chronopl() has been improved and gains several options: see its
-      help page for details.
+    o seg.sites() failed with a list.
+
+    o consensus() failed in some cases. The function has been improved
+      as well and is faster.