new option 'draw' in plot.phylo()

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index 32f99c176f5c57989b540425499eea13c3700a6b..c702b68074489aa961044ce2efd6819da03b96c4 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,4 +1,54 @@
-               CHANGES IN APE VERSION 2.6-4
+               CHANGES IN APE VERSION 2.7-2
+
+
+NEW FEATURES
+
+    o plot.phylo() has a new option 'draw = TRUE'. If FALSE, the tree
+      is not plotted but the graphical device is set and the
+      coordinates are saved as normal.
+
+
+
+               CHANGES IN APE VERSION 2.7-1
+
+
+NEW FEATURES
+
+    o The new function trex does tree exploration with multiple
+      graphical devices.
+
+    o The new function kronoviz plots several rooted (dated) trees on
+      the scale scale.
+
+    o identify.phylo() has a new option 'quiet' (FALSE by default).
+
+
+BUG FIXES
+
+    o A bug was introduced in read.nexus() in ape 2.7.
+
+    o image.DNAbin() did not colour correctly the bases if there were
+      some '-' and no 'N'.
+
+    o .compressTipLabel() failed with a list with a single tree.
+
+    o identify.phylo() returned a wrong answer when the x- and y-scales
+      are very different.
+
+    o write.nexus() failed with lists of trees with compressed labels.
+
+
+OTHER CHANGES
+
+    o identify.phylo() now returns NULL if the user right-(instead of
+      left-)clicks (an error was returned previously).
+
+    o read.nexus() should be robust to commands inserted in the TREES
+      block.
+
+
+
+               CHANGES IN APE VERSION 2.7
 
 
 NEW FEATURES
@@ -6,11 +56,23 @@ NEW FEATURES
     o There is a new image() method for "DNAbin" objects: it plots DNA
       alignments in a flexible and efficient way.
 
+    o Two new functions as.network.phylo and as.igraph.phylo convert
+      trees of class "phylo" into these respective network classes
+      defined in the packages of the same names.
+
+    o The three new functions clustal, muscle, and tcoffee perform
+      nucleotide sequence alignment by calling the external programs
+      of the same names.
+
+    o Four new functions, diversity.contrast.test, mcconwaysims.test,
+      richness.yule.test, and slowinskiguyer.test, implement various
+      tests of diversification shifts using sister-clade comparisons.
+
     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 list
-      of trees with names.
+    o read.nexus() now writes tree names in the NEXUS file if given a
+      list of trees with names.
 
 
 BUG FIXES