bug corrected in del.gaps + small change in man page of theta.s

[ape.git] / Changes

diff --git a/Changes b/Changes
index 2fe5b8d492ef56e7adbaa934e1a44a729492b162..854ae1949d3b84ed1ca5e8ade91a4cf660ef94a2 100644 (file)
--- a/Changes
+++ b/Changes
@@ -12,6 +12,23 @@ BUG FIXES
     o prop.part() failed with a single tree with the default option
      'check.labels = TRUE'.
 
+   o summary.DNAbin() failed to display correctly the summary of
+     sequence lengths with lists of sequences of 10,000 bases or more
+     (because summary.default uses 4 significant digits by default).
+
+   o read.nexus() failed to read a file with a single tree with line
+     breaks in the Newick string.
+
+   o del.gaps() returned a list of empty sequences when there were no
+     gaps.
+
+
+OTHER CHANGES
+
+    o The data sets bird.orders and bird.families are now stored as
+      Newick strings; i.e., the command data(bird.orders) calls
+      read.tree().
+
 
 
                CHANGES IN APE VERSION 2.2-1
@@ -241,9 +258,9 @@ BUG FIXES
 
 OTHER CHANGES
 
-    o The code of mlphylo() has almost entirely rewritten, and should
-      be much stabler. The options have been also greatly simplified
-      (see ?mlphylo and ?DNAmodel for details).
+    o The code of mlphylo() has been almost entirely rewritten, and
+      should be much stabler. The options have been also greatly
+      simplified (see ?mlphylo and ?DNAmodel for details).
 
     o The internal function nTips has been renamed klastorin_nTips.