X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=a635615eecbe29422c094b6ce0daee4177b9e068;hb=453ad4ce9e573998f28185d92c8d71367dd32f23;hp=a4985e5dfcc71b19f3d191007abe15da6ec9bbab;hpb=6603d33385e67db10a1d48f3ab7ec1910ce295ca;p=ape.git

diff --git a/ChangeLog b/ChangeLog
index a4985e5..a635615 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,50 @@
+		CHANGES IN APE VERSION 2.6-4
+
+
+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 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.
+
+
+BUG FIXES
+
+    o prop.part() failed in some situations with unrooted trees.
+
+    o read.nexus() shuffled node labels when a TRANSLATE block was
+      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
+
+    o BaseProportion in src/dist_dna.c has been modified.
+
+    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 redundant.
+
+
+
 		CHANGES IN APE VERSION 2.6-3
 
 
@@ -17,11 +64,22 @@ BUG FIXES
     o read.dna(, "fasta") failed if sequences were not all of the same
       length.
 
+    o plot.phylo() did not recycle values of 'font', 'cex' and
+      'tip.color' correctly when type = "fan" or "radial".
+
+    o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or
+      "unrooted" with lab4ut = "axial" (the placement of tip labels still
+      needs to be improved with lab4ut = "horizontal").
+
 
 OTHER CHANGES
 
     o In drop.fossil() the default tol = 0 has been raised to 1e-8.
 
+    o The help command ?phylo now points to the man page of read.tree()
+      where this class is described. Similarly, ?matching points to the
+      man page of as.matching().
+
 
 
 		CHANGES IN APE VERSION 2.6-2