X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=c88556f37ac0c9cc7505097d2dba56924c785247;hb=bfaeca35ec130110327a3bb7a1f0fe3b66076a95;hp=53f4a6209d15230d3dbb36932f60b65c3c173daa;hpb=57c9d4fd10a4449c27c65873eaf9315b5b7ed874;p=ape.git

diff --git a/ChangeLog b/ChangeLog
index 53f4a62..c88556f 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,10 +1,69 @@
+		CHANGES IN APE VERSION 2.6-4
+
+
+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 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
+
+
+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 repetitive.
+
+
+
 		CHANGES IN APE VERSION 2.6-3
 
 
+NEW FEATURES
+
+    o rTraitCont() and rTraitDisc() gains a '...' argument used with
+      user-defined models (suggestion by Gene Hunt).
+
+
 BUG FIXES
 
     o as.hclust.phylo() now returns an error with unrooted trees.
 
+    o as.hclust.phylo() failed with trees with node labels (thanks to
+      Jinlong Zhang for pointing this bug out).
+
+    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