NEWS.md

In ips: Interfaces to Phylogenetic Software in R

ips 0.0.12

New features

• 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.

ips 0.0.11

New features

• forceEqualTipHeights() corrects small rounding errors in edge lengths such that the resulting phylogeny will pass ape::is.ultrametric().

Improved features

• 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)

ips 0.0-10

Improved features

• 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.

ips 0.0-9

Improved features

• 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.

Deprecated features

• write.partioned.nex() was removed from the package; its functionality has been integrated into write.nex().

ips 0.0-8

Improved features

• 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.

Deprecated features

• write.partioned.nex() will be removed soon from the package; its functionality has been integrated into write.nex().

Bug fixes

• Argument run = TRUE in mrbayes() and mrbayes.mixed() was broken on Windows platforms. (Thanks to Liam Revell and Klaus Schliep for report and fix).

ips 0.0-7

New features

• 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 (\url{https://mafft.cbrc.jp/alignment/software/newick2mafft.rb}): 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.

Deprecated features

• 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.

ips documentation built on May 29, 2024, 4:39 a.m.