+ CHANGES IN APE VERSION 2.2-2
+
+
+NEW FEATURES
+
+ o dist.gene() has been substantially improved and gains an option
+ 'pairwise.deletion'.
+
+
+BUG FIXES
+
+ o prop.part() failed with a single tree with the default option
+ 'check.labels = TRUE'.
+
+
+OTHER CHANGES
+
+ o The data sets bird.orders and bird.families are now stored as
+ Newick strings; e.g., the command data(bird.orders) calls
+ read.tree().
+
+
+
CHANGES IN APE VERSION 2.2-1
NEW FEATURES
+ o The new function makeLabel() helps to modify labels of trees,
+ lists of trees, or DNA sequences, with several utilities to
+ truncate and/or make them unique, substituting some
+ characters, and so on.
+
o The new function del.gaps() removes insertion gaps ("-") in a
set of DNA sequences.
+ o read.dna() can now read Clustal files (*.aln).
+
+
+BUG FIXES
+
+ o root() failed with 'resolve.root = TRUE' when the root was
+ already the specified root.
+
+ o Several bugs were fixed in mlphylo().
+
+ o collapsed.singles() did not propagate the 'Nnode' and
+ 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
+
+ o read.nexus() failed to remove correctly the comments within
+ trees.
+
+ o read.nexus() failed to read a file with a single tree and no
+ translation of tip labels.
+
+ o read.nexus() failed to place correctly tip labels when reading
+ a single tree with no edge lengths.
+
+ o A bug was fixed in sh.test().
+
OTHER CHANGES
o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
Minin.
+ o The option 'check.labels' of consensus() and prop.part() is now
+ TRUE by default.
+
+ o write.dna() now does not truncate names to 10 characters with
+ the Phylip formats.
+
CHANGES IN APE VERSION 2.2
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.