X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=ec8918ae97f2c4e7d9bfe7e8a7d19fc2a6599041;hb=4302b11b3ae487613d8f9480dfb86a840087b343;hp=53eb924bb2734247fdcdc6ac271698869bb7d741;hpb=fab4946bb5d41cd408dffd4b66aae8a697690cfa;p=ape.git

diff --git a/NEWS b/NEWS
index 53eb924..ec8918a 100644
--- a/NEWS
+++ b/NEWS
@@ -1,10 +1,131 @@
+		CHANGES IN APE VERSION 3.0-5
+
+
+OTHER CHANGES
+
+    o write.dna(format = "fasta") now conforms more closely to the
+      FASTA standard thanks to François Michonneau.
+
+    o print.DNAbin() does not print base compositions if there are more
+      than one million nucleotides.
+
+
+
+		CHANGES IN APE VERSION 3.0-4
+
+
+BUG FIXES
+
+    o read.dna() failed to read Phylip files if the first line used
+      tabulations instead of white spaces.
+
+    o read.dna() failed to read Phylip or Clustal files with less than
+      10 nucleotides. (See other changes in this function below.)
+
+OTHER CHANGES
+
+    o read.dna() now requires at least one space (or tab) between the
+      taxa names and the sequences (whatever the length of taxa
+      names). write.dna() now follows the same rule.
+
+    o The option 'seq.names' of read.dna has been removed.
+
+    o The files ape-defunct.R and ape-defunct.Rd, which have not been
+      modified for almost two years, have been removed.
+
+    o The C code of bionj() has been reworked: it is more stable (by
+      avoiding passing character strings), slightly faster (by about
+      20%), and numerically more accurate.
+
+    o The C code of fastme.*() has been slightly modified and should
+      be more stable by avoiding passing character strings (the
+      results are identical to the previous versions).
+
+    o The file src/newick.c has been removed.
+
+
+
+		CHANGES IN APE VERSION 3.0-3
+
+
+BUG FIXES
+
+    o birthdeath() now catches errors and warnings much better so that
+      a result is returned in most cases.
+
+
+OTHER CHANGES
+
+    o Because of problems with character string manipulation in C, the
+      examples in ?bionj and in ?fastme have been disallowed. In the
+      meantime, these functions might be unstable. This will be solved
+      for the next release.
+
+
+
+		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.
+
+
+BUG FIXES
+
+    o compute.brtime() did not completely randomized the order of the
+      branching times.
+
+    o write.nexus() did not work correctly with rooted trees (thanks
+      to Matt Johnson for the fix).
+
+    o mltt.plot(, backward = FALSE) did not set the x-axis correctly.
+
+    o A bug was introduced in prop.clades() with ape 3.0. The help page
+      has been clarified relative to the use of the option 'rooted'.
+
+    o mantel.test() printed a useless warning message.
+
+    o plot.phylo(, direction = "downward") ignored 'y.lim'.
+
+    o is.monophyletic() did not work correctly if 'tips' was not stored
+      as integers.
+
+    o prop.part() could make R crash if the first tree had many
+      multichotomies.
+
+    o njs(), bionjs(), and mvrs() now return an error if 'fs < 1'.
+
+    o SDM() did not work correctly. The code has also been generally
+      improved.
+
+
+OTHER CHANGES
+
+    o The DESCRIPTION file has been updated.
+
+    o The option 'original.data' of write.nexus() has been removed.
+
+    o The files bionjs.c, mvr.c, mvrs.c, njs.c, triangMtd.c, and
+      triangMtds.c have been improved which should fix some bugs in
+      the corresponding functions.
+
+    o dist.gene() now coerces input data frame as matrix resulting in
+      much faster calculations (thanks to a suggestion by Markus
+      Schlegel).
+
+
+
 		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 lengths permitting to create a node in 'x' when grafting
+      banch length permitting to create a node in 'x' when grafting
       'y' (see ?bind.tree for details).
 
 
@@ -13,6 +134,11 @@ 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