+ 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 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
+
+
+NEW FEATURES
+
+ o Two new functions, pic.ortho and varCompPhylip, implements the
+ orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The
+ second function requires Phylip to be installed on the computer.
+
+ o bd.ext() has a new option conditional = TRUE to use probabilities
+ conditioned on no extinction for the taxonomic data.
+
+
+BUG FIXES
+
+ o write.tree() failed to output correctly tree names.
+
+ o dist.nodes() returned duplicated column(s) with unrooted and/or
+ multichotomous trees.
+
+ o mcmc.popsize() terminated unexpectedly if the progress bar was
+ turned off.
+
+ o prop.part(x) made R frozen if 'x' is of class "multiPhylo".
+
+ o Compilation under Mandriva failed (thanks to Jos Käfer for the fix).
+
+ o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal
+ = FALSE.
+
+ o Objects returned by as.hclust.phylo() failed when analysed with
+ cutree() or rect.hclust().
+
+ o write.tree() did not output correctly node labels (thanks to Naim
+ Matasci and Jeremy Beaulieu for the fix).
+
+ o ace(type = "discrete") has been improved thanks to Naim Marasci and
+ Jeremy Beaulieu.
+
+
+
CHANGES IN APE VERSION 2.6-1
+NEW FEATURES
+
+ o The new function speciesTree calculates the species tree from a set
+ of gene trees. Several methods are available including maximum tree
+ and shallowest divergence tree.
+
+
BUG FIXES
+ o A bug introduced in write.tree() with ape 2.6 has been fixed.
+
o as.list.DNAbin() did not work correctly with vectors.
o as.hclust.phylo() failed with trees with node labels (thanks to
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.
+ o write.tree() and read.tree() have been substantially improved thanks
+ to contributions by Klaus Schliep.
projects / ape.git / blobdiff