new code for reading FASTA files

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index 812bb6c414cdbf2a9e8f3b54bbbb63b0e711c441..57d1924cccdeffb9e41b43d9a2934a04ebe6aa68 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,6 +1,71 @@
+               CHANGES IN APE VERSION 3.0-7
+
+
+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 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
 
 
+NEW FEATURES
+
+    o reorder.phylo() has a new order, "postorder", and a new option
+      index.only = TRUE to return only the vector of indices (the tree
+      is unmodified, see ?reorder.phylo for details).
+
+    o The three new functions node.depth.edgelength, node.height, and
+      node.height.clado make some internal code available from R. See
+      ?node.depth (which was already documented) for details.
+
+
+BUG FIXES
+
+    o reorder(, "pruningwise") made R crash if the rows of the edge
+      matrix are in random order: this is now fixed.
+
+    o drop.tip() sometimes shuffled node labels (thanks to Rebecca
+      Best for the report).
+
+    o drop.tip(phy, "") returned a tree with zero-length tip labels:
+      it now returns the tree unchanged (thanks to Brian Anacker for
+      the report).
+
+    o plot.phylo() made R crash if the tree has zero-length tip
+      labels: it now returns NULL (thanks again to Brian Anacker).
+
+
 OTHER CHANGES
 
     o dist.nodes() is now 6 to 10 times faster.
@@ -9,6 +74,14 @@ OTHER CHANGES
       visible for small trees (n < 1000) but this can be more than
       1000 faster for big trees (n >= 1e4).
 
+    o The attribute "order" of the objects of class "phylo" is now
+      strongly recommended, though not mandatory. Most functions in
+      ape should return a tree with this attribute correctly set.
+
+    o dbd() is now vectorized on both arguments 'x' (number of species
+      in clade) and 't' (clade age) to make likelihood calculations
+      easier and faster.
+
 
 
                CHANGES IN APE VERSION 3.0-5
@@ -1943,14 +2016,14 @@ BUG FIXES
     o A bug was fixed in phymltest(): the executable couldn't be found
       in some cases.
 
-    o Three bug have been fixed in ace(): computing the likelihood of
+    o Three bugs have been fixed in ace(): computing the likelihood of
       ancestral states of discrete characters failed, custom models
       did not work, and the function failed with a null gradient (a
       warning message is now returned; this latter bug was also
       present in yule.cov() as well and is now fixed).
 
-    o pic() hanged out when missing data were present: a message error
-      is now returned.
+    o pic() hanged out when missing data were present: an error is now
+      returned.
 
     o A small bug was fixed in dist.dna() where the gamma correction
       was not always correctly dispatched.
@@ -2014,7 +2087,7 @@ NEW FEATURES
       DNA sequences by specifying model = "raw".
 
     o dist.phylo() has a new option `full' to possibly compute the
-      distances among all tips and nodes of the tree. The default if
+      distances among all tips and nodes of the tree. The default is
       `full = FALSE'.