X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=678bba7b17c60151cf7e1dd0924e69c7ae72341e;hb=f512087dd94a7dc3462a9f31b48f61214cdc0f5e;hp=a1c4552b70cff150d4a02cc5c6f635288f82d789;hpb=8583b8f50f7747a557dbaf6678207da5108087f9;p=ape.git

diff --git a/ChangeLog b/ChangeLog
index a1c4552..678bba7 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,36 @@
+		CHANGES IN APE VERSION 2.3-3
+
+
+BUG FIXES
+
+    o 
+
+
+
+		CHANGES IN APE VERSION 2.3-2
+
+
+BUG FIXES
+
+    o all.equal.phylo() did not compare unrooted trees correctly.
+
+    o dist.topo(... method = "PH85") did not treat unrooted trees
+      correctly (thanks to Tim Wallstrom for the fix).
+
+    o root() sometimes failed to test for the monophyly of the
+      outgroup correctly.
+
+    o extract.clade() sometimes included too many edges.
+
+    o vcv.phylo() did not work correctly when the tree is in
+      "pruningwise" order.
+
+    o nj() did not handle correctly distance matrices with many 0's.
+      The code has also been significantly improved: 7, 70, 160 times
+      faster with n = 100, 500, 1000, respectively.
+
+
+
 		CHANGES IN APE VERSION 2.3-1
 
 
@@ -10,6 +43,9 @@ NEW FEATURES
     o yule.cov() now fits the null model, and its help page has been
       corrected with respect to this change.
 
+    o drop.tip() has a new option 'rooted' to force (or not) a tree
+      to be treated as (un)rooted.
+
 
 BUG FIXES
 
@@ -30,6 +66,8 @@ BUG FIXES
 
     o write.tree() failed with objects of class "multiPhylo".
 
+    o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
+
 
 OTHER CHANGES