new files for ape 3.0

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index cc8d3af63c727603a15bf1ce227de83a0a10eace..0ca6a14ff076ca1681992b5e4fb3cd9aacfaadb2 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,10 +1,19 @@
-               CHANGES IN APE VERSION 2.8-1
+               CHANGES IN APE VERSION 3.0
 
 
 NEW FEATURES
 
+    o The three functions dyule, dbd, and dbdTime calculate the
+      density probability (i.e., the distribution of the number of
+      species) for the Yule, the constant and the time-dependent
+      birth-beath models, respectively. These probabilities can be
+      conditional on no extinction and/or on a log-scale.
+
     o plot.phylo() has a new option 'rotate.tree' to rotate unrooted,
-      fan or radial trees around the center of the plot.
+      fan, or radial trees around the center of the plot.
+
+    o boot.phylo() and prop.clades() have a new option rooted =
+      FALSE. Note that the behaviour of prop.part() is unchanged.
 
 
 BUG FIXES
@@ -15,6 +24,8 @@ BUG FIXES
     o extract.clade() sometimes shuffled some tip labels (thanks to
       Ludovic Mallet and Mahendra Mariadassou for the fix).
 
+    o clustal() should now find by default the executable under Windows.
+
 
 OTHER CHANGES
 
@@ -24,6 +35,9 @@ OTHER CHANGES
     o The code of mantel.test() has been adjusted to be consistent
       with common permutation tests.
 
+    o The C code of base.freq() has been improved and is now nearly 8
+      times faster.
+
 
 
                CHANGES IN APE VERSION 2.8