some modifs for ape 3.0-8

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index f6acbff8297c3c3756acc8ec24a2db1115399c7d..5f1d7589aafb9c97738201ad10ea1874273099a7 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,8 +1,29 @@
+               CHANGES IN APE VERSION 3.0-8
+
+
+NEW FEATURES
+
+    o ace() gains a new option 'use.expm' to use expm() from the
+      package of the same name in place of matexpo().
+
+
+BUG FIXES
+
+    o read.dna(, "fasta") may add '\r' in labels: this is fixed.
+
+
+
                CHANGES IN APE VERSION 3.0-7
 
 
 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
@@ -15,6 +36,10 @@ NEW FEATURES
     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
 
@@ -28,6 +53,11 @@ 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.
+
 
 
                CHANGES IN APE VERSION 3.0-6
@@ -468,7 +498,7 @@ 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.