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The new function forceEqualTipHeights corrects small rounding errors in edge lengths such that the resulting phylogeny will pass ape::is.ultrametric.
The new argument 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)
The new argument 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 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.
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.
The argument run = TRUE in functions mrbayes and mrbayes.mixed was broken on Windows platforms. (Thanks to Liam Revell and Klaus Schliep for report ans fix).
The function 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.
The functions delete.empty.cells and fillEndsWithN are now using Emanuel Paradis' bit-level coding for DNA sequences, which makes them much faster.
The function 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.