new code for reading FASTA files

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index 9d57433878a743da5cbd7fd9481b4bc14a80bfc0..57d1924cccdeffb9e41b43d9a2934a04ebe6aa68 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -6,13 +6,34 @@ NEW FEATURES
     o The new function 'where' searches patterns in DNA sequences.
 
     o pic() gains an option 'rescaled.tree = FALSE' to return the tree
-      with its branch lengths rescaled for the PICs calculation.
+      with its branch lengths rescaled for the PIC calculation.
+
+    o clustal(), muscle(), and tcoffee() gain an option
+      'original.ordering = TRUE' to ease the comparisons of
+      alignments.
+
+    o plot.phylo() has a new option, open.angle, used when plotting
+      circular trees.
+
+    o The new function read.FASTA reads FASTA files much faster and
+      more efficiently. It is called internally by read.dna(, "fasta")
+      or can be called directly.
 
 
 BUG FIXES
 
     o drop.tip() shuffled node labels on some trees.
 
+    o axisPhylo() now works correctly with circular trees, and gives a
+      sensible error message when type = "r" or "u".
+
+
+OTHER CHANGES
+
+    o .compressTipLabel() is 10 times faster thanks to Joseph Brown.
+
+    o base.freq() is now faster with lists.
+
 
 
                CHANGES IN APE VERSION 3.0-6