some updates for ape 3.0-7

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index 442534831a83410208674241b0d5746377ef726e..6c871841b94dba7d480bd99264ea9c43de64b3a3 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -3,14 +3,49 @@
 
 NEW FEATURES
 
+    o The new function chronos estimates chronograms by penalised
+      likelihood and maximum likelihood with a completely reworked
+      code and interface. There is a new function makeChronosCalib to
+      set the calibration points easily. chronos() will eventually
+      replace chronopl().
+
+    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.
+
+    o as.matrix.DNAbin() should be faster and more efficient with
+      lists; it now accepts vectors.
+
+    o collapse.singles() is faster thanks to Klaus Schliep. This will
+      speed-up drop.tip() significantly.
+
 
 
                CHANGES IN APE VERSION 3.0-6
@@ -451,7 +486,7 @@ NEW FEATURES
     o base.freq() gains an option 'all' to count all the possible bases
       including the ambiguous ones (defaults to FALSE).
 
-    o read.nexus() now writes tree names in the NEXUS file if given a
+    o write.nexus() now writes tree names in the NEXUS file if given a
       list of trees with names.