some updates for ape 3.0-7

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index 1f2cd220f396a79f3bc7b53b25555fa3bf2a683c..6c871841b94dba7d480bd99264ea9c43de64b3a3 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -3,7 +3,11 @@
 
 NEW FEATURES
 
-      The new function chronos ..........
+    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.
 
@@ -36,9 +40,11 @@ OTHER CHANGES
 
     o base.freq() is now faster with lists.
 
-      as.matrix.DNAbin() ............ should be faster.... now accepts vectors,
+    o as.matrix.DNAbin() should be faster and more efficient with
+      lists; it now accepts vectors.
 
-      read.dna() has a new for FASTA files............. faster C code.
+    o collapse.singles() is faster thanks to Klaus Schliep. This will
+      speed-up drop.tip() significantly.
 
 
 
@@ -480,7 +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.