blastn() provides an interface to the command-line
program blastn for nucleotide to nucleotide comparison.
combMyTree() grafts polytomies on a
phylogeny.
deleteEmptyCells() has now a sister function
identifyEmtpyCells() that won’t delete but only identify
the empty rows and columns in a sequence alignment. This is useful if
there is a second matrix (e.g. with confidence scores) tied to the
sequence alignment.
forceEqualTipHeights() corrects small rounding errors
in edge lengths such that the resulting phylogeny will pass
ape::is.ultrametric().weights in raxml() allows to
assign individual weights to each column of the alignment. It
corresponds to the -a flag in RAxML (see The RAxML v8.2.x Manual for
details)exec in mrbayes() allows to
specify the name and path of the MrBayes executable explicitly. If the
executable is in the search path, exec can be missing.write.nex() and matrixBlock were extended
to handle standard (morphological, etc.) data in a data frame. This
feature including the coding of ambiguous characters was tested
successfully with MrBayes.write.partioned.nex() was removed from the package; its
functionality has been integrated into write.nex().write.nex() can now handle multiple DNA sequence
alignments.
Argument interleave of functions
write.fas(), write.phy(), and
write.nex() has been renamed to block.width
for clarity.
write.partioned.nex() will be removed soon from the
package; its functionality has been integrated into
write.nex().run = TRUE in mrbayes() and
mrbayes.mixed() was broken on Windows platforms. (Thanks to
Liam Revell and Klaus Schliep for report and fix).mafft() received the additional argument
options, which can be used to request options such as
e.g. --adjustdirection that are not build into the
function’s interface.
This version includes a new internal function
phylo2mafft(), which does exactly the same thing as the
RUBY script newick2mafft.rb on the MAFFT website (): it
converts a user-defined guide tree into a format readible by
MAFFT.
delete.empty.cells() and
fillEndsWithN() are now using Emanuel Paradis’ bit-level
coding for DNA sequences, which makes them much faster.
c.genes() has been superseeded by the cbind method for
objects of class "DNAbin" provided in the package
ape; c.genes() will be removed in one of
the following versions.