bug fixed in write.tree

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index 5a6817e06a65c287771809a14472393a88a7fe2c..69c19c3a7f200c10591a523c3c074b532b64437d 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,39 @@
+               CHANGES IN APE VERSION 2.6-2
+
+
+NEW FEATURES
+
+    o bd.ext() has a new option conditional = TRUE to use probabilities
+      conditioned on no extinction for the taxonomic data.
+
+
+BUG FIXES
+
+    o write.tree() failed to output correctly tree names.
+
+
+
+               CHANGES IN APE VERSION 2.6-1
+
+
+NEW FEATURES
+
+    o The new function speciesTree calculates the species tree from a set
+      of gene trees. Several methods are available including maximum tree
+      and shallowest divergence tree.
+
+
+BUG FIXES
+
+    o A bug introduced in write.tree() with ape 2.6 has been fixed.
+
+    o as.list.DNAbin() did not work correctly with vectors.
+
+    o as.hclust.phylo() failed with trees with node labels (thanks to
+      Filipe Vieira for the fix).
+
+
+
                CHANGES IN APE VERSION 2.6
 
 
@@ -5,11 +41,15 @@ NEW FEATURES
 
     o The new functions rlineage and rbdtree simulate phylogenies under
       any user-defined time-dependent speciation-extinction model. They
-      use new continuous time algorithms.
+      use continuous time algorithms.
 
     o The new function drop.fossil removes the extinct species from a
       phylogeny.
 
+    o The new function bd.time fits a user-defined time-dependent
+      birth-death model. It is a generalization of yule.time() taking
+      extinction into account.
+
     o The new function MPR does most parsimonious reconstruction of
       discrete characters.
 
@@ -53,6 +93,9 @@ OTHER CHANGES
     o pic() now returns a vector with the node labels of the tree (if
       available) as names.
 
+    o write.tree() and read.tree() have been substantially improved thanks
+      to contributions by Klaus Schliep.
+
 
 
                CHANGES IN APE VERSION 2.5-3