+ CHANGES IN APE VERSION 2.2-2
+
+
+NEW FEATURES
+
+ o dist.gene() has been substantially improved and gains an option
+ 'pairwise.deletion'.
+
+
+
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 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 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
Minin.
o The option 'check.labels' of consensus() and prop.part() is now
- TRUE.
+ TRUE by default.
+
+ o write.dna() now does not truncate names to 10 characters with
+ the Phylip formats.