new pic.ortho() and varCompPhylip() + fix in dist.nodes()

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index abb26160fda15c623d83ff7f149271973307cf58..94d9816f25afd2f3ca0a76b58d2918b99f01788e 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,46 @@
+               CHANGES IN APE VERSION 2.6-2
+
+
+NEW FEATURES
+
+    o Two new functions, pic.ortho and varCompPhylip, implements the
+      orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
+      second function requires Phylip to be installed on the computer.
+
+    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.
+
+    o dist.nodes() returned duplicated column(s) with unrooted and/or
+      multichotomous trees.
+
+
+
+               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
 
 
@@ -57,6 +100,9 @@ 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