X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Changes;h=f8562e43cd76dbd0cf09154e6a382422054c1fea;hb=62ec445353b420aac117855ff989dfcdce19f068;hp=729a2530b6b39bb6b1e8db23cc7d8d951e35c1ca;hpb=ba59c6508990bce5fa5071c0fb346e39d2b2a325;p=ape.git

diff --git a/Changes b/Changes
index 729a253..f8562e4 100644
--- a/Changes
+++ b/Changes
@@ -1,4 +1,40 @@
-		CHANGES IN APE VERSION 2.1-4
+		CHANGES IN APE VERSION 2.2-1
+
+
+NEW FEATURES
+
+    o The new function del.gaps() removes insertion gaps ("-") in a
+      set of DNA sequences.
+
+
+OTHER CHANGES
+
+    o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
+      Minin.
+
+
+
+		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
@@ -9,13 +45,18 @@ BUG FIXES
     o The x/y aspect of the plot is now respected when plotting a
       circular tree (type = "r" or "f").
 
-    o Drawing the tip labels sometimes when plotting circular trees.
+    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.