a bunch of new stuff (see ChangeLog)

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index 057cf583a570dd78448d2e318059d3aaadd33e53..a635615eecbe29422c094b6ce0daee4177b9e068 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,87 @@
+               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
+
+
+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
 
 
@@ -32,7 +116,10 @@ BUG FIXES
       cutree() or rect.hclust().
 
     o write.tree() did not output correctly node labels (thanks to Naim
-      Matasci for the fix).
+      Matasci and Jeremy Beaulieu for the fix).
+
+    o ace(type = "discrete") has been improved thanks to Naim Marasci and
+      Jeremy Beaulieu.