new speciesTree()

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
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+++ b/ChangeLog
@@ -1,8 +1,44 @@
-               CHANGES IN APE VERSION 2.5-4
+               CHANGES IN APE VERSION 2.6-1
 
 
 NEW FEATURES
 
+    o The new speciesTree calculates the species tree from a set of gene
+      trees. Two methods are currently available: maximum tree and
+      shallowest divergence tree.
+
+
+BUG FIXES
+
+    o as.list.DNAbin() did not work correctly with vectors.
+
+    o as.hclust.phylo() failed with trees with node labels (thanks to
+      Filipe Vieira for the fix).
+
+
+
+               CHANGES IN APE VERSION 2.6
+
+
+NEW FEATURES
+
+    o The new functions rlineage and rbdtree simulate phylogenies under
+      any user-defined time-dependent speciation-extinction model. They
+      use continuous time algorithms.
+
+    o The new function drop.fossil removes the extinct species from a
+      phylogeny.
+
+    o The new function bd.time fits a user-defined time-dependent
+      birth-death model. It is a generalization of yule.time() taking
+      extinction into account.
+
+    o The new function MPR does most parsimonious reconstruction of
+      discrete characters.
+
+    o The new function Ftab computes the contingency table of base
+      frequencies from a pair of sequences.
+
     o There is now an 'as.list' method for the class "DNAbin".
 
     o dist.dna() can compute the number of transitions or transversions
@@ -12,6 +48,37 @@ NEW FEATURES
       control the aspect of thermometers: horiz = TRUE, width = NULL,
       and height = NULL.
 
+    o compar.gee() has been improved with the new option 'corStruct' as an
+      alternative to 'phy' to specify the correlation structure, and
+      calculation of the QIC (Pan 2001, Biometrics). The display of the
+      results has also been improved.
+
+    o read.GenBank() has a new option 'gene.names' to return the name of
+      the gene (FALSE by default).
+
+
+BUG FIXES
+
+    o extract.clade() sometimes shuffled the tip labels.
+
+    o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus
+      Schliep for the fix)
+
+    o dist.dna(model = "logdet") used to divide distances by 4. The
+      documentation has been clarified on the formulae used.
+
+
+OTHER CHANGES
+
+    o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly
+      change the parameterisation (see ?rTraitCont for details).
+
+    o pic() now returns a vector with the node labels of the tree (if
+      available) as names.
+
+    o write.tree() and read.tree() have been substantially thanks to
+      contributions by Klaus Schliep.
+
 
 
                CHANGES IN APE VERSION 2.5-3