new alex()

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index 55d0adc836df886582039bfc36a8f2d039694ada..2ebf72e906fb998d185d1c717e7ef728a5766255 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,21 +1,72 @@
+               CHANGES IN APE VERSION 3.0-2
+
+
+NEW FEATURES
+
+    o The new function alex (alignment explorator) zooms in a DNA
+      alignment and opens the result in a new window.
+
+
+
+               CHANGES IN APE VERSION 3.0-1
+
+
+NEW FEATURES
+
+    o dist.dna() has two new models: "indel" and "indelblock".
+
+    o bind.tree() now accepts 'position' > 0 when the trees have no
+      banch length permitting to create a node in 'x' when grafting
+      'y' (see ?bind.tree for details).
+
+
+BUG FIXES
+
+    o cophyloplot( , rotate = TRUE) made R hanged after a few clicks.
+      Also the tree is no more plotted twice.
+
+    o read.GenBank() has been updated to work with EFetch 2.0.
+
+    o unroot() on trees in "pruningwise" order did not respect this
+      attribute
+
+
+
                CHANGES IN APE VERSION 3.0
 
 
 NEW FEATURES
 
+    o The three functions dyule, dbd, and dbdTime calculate the
+      density probability (i.e., the distribution of the number of
+      species) for the Yule, the constant and the time-dependent
+      birth-beath models, respectively. These probabilities can be
+      conditional on no extinction and/or on a log-scale.
+
     o plot.phylo() has a new option 'rotate.tree' to rotate unrooted,
-      fan or radial trees around the center of the plot.
+      fan, or radial trees around the center of the plot.
+
+    o boot.phylo() and prop.clades() have a new option rooted =
+      FALSE. Note that the behaviour of prop.part() is unchanged.
+
+    o edgelabels() has a new option 'date' to place labels on edges of
+      chronograms using the time scale (suggestion by Rob Lanfear).
 
 
 BUG FIXES
 
-    o mantel.test() could return P-values > 1 with the default
+    o In chronopl(), the code setting the initial dates failed in
+      complicated settings (several dates known within intervals).
+      This has been generally improved and should result in faster
+      and more efficient convergence even in simple settings.
+
+    o mantel.test() sometimes returned P-values > 1 with the default
       two-tailed test.
 
     o extract.clade() sometimes shuffled some tip labels (thanks to
       Ludovic Mallet and Mahendra Mariadassou for the fix).
 
-    o clustal() should now by default find the executable under Windows.
+    o clustal() should now find by default the executable under Windows.
 
 
 OTHER CHANGES
@@ -29,6 +80,16 @@ OTHER CHANGES
     o The C code of base.freq() has been improved and is now nearly 8
       times faster.
 
+    o The option 'original.data' of write.nexus() is now deprecated and
+      will be removed in a future release.
+
+    o The code of is.ultrametric() has been improved and is now 3 times
+      faster.
+
+    o The code of vcv.phylo() has been improved and is now 10 or 30
+      times faster for 100 or 1000 tips, respectively. Consequently,
+      fitting models with PGLS will be faster overall.
+
 
 
                CHANGES IN APE VERSION 2.8
@@ -182,8 +243,8 @@ BUG FIXES
 
 OTHER CHANGES
 
-    o identify.phylo() now returns NULL if the user right-(instead of
-      left-)clicks (an error was returned previously).
+    o identify.phylo() now returns NULL if the user right- (instead of
+      left-) clicks (an error was returned previously).
 
     o read.nexus() should be robust to commands inserted in the TREES
       block.