The new function
forceEqualTipHeights corrects small rounding errors in edge lengths such that the resulting phylogeny will pass
The new argument
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)
The new argument
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.
matrixBlocks) 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 can now handle multiple DNA sequence alignments.
interleave of functions
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
run = TRUE in functions
mrbayes.mixed was broken on Windows platforms. (Thanks to Liam Revell and Klaus Schliep for report ans 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 (http://mafft.cbrc.jp/alignment/software/newick2mafft.rb): it converts a user-defined guide tree into a format readible by MAFFT.
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 object of class
"DNAbin" provided in the package ape;
c.genes will be removed in one of the following versions.