final packing for ape 2.7

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index c88556f37ac0c9cc7505097d2dba56924c785247..eb386db6d31e34f9f896d3b5664ff61235ada3b8 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,13 +1,28 @@
-               CHANGES IN APE VERSION 2.6-4
+               CHANGES IN APE VERSION 2.7
 
 
 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
@@ -15,7 +30,12 @@ BUG FIXES
     o prop.part() failed in some situations with unrooted trees.
 
     o read.nexus() shuffled node labels when a TRANSLATE block was
-      present
+      present.
+
+    o varCompPhylip() did not work if 'exec' was specified.
+
+    o bind.tree() shuffled node labels when position > 0 and 'where'
+      was not the root.
 
 
 OTHER CHANGES
@@ -25,7 +45,7 @@ OTHER CHANGES
     o A number of functions in src/tree_build.c have been modified.
 
     o The matching representation has now only two columns as the third
-      column was repetitive.
+      column was redundant.