A new phytools version (phytools 0.4-56) is now on CRAN. As of writing, Mac & Windows binaries had not yet been built. Hopefully those will be available, and will begin to percolate through the mirror repositories, within a few days.
Among the updates in this version are the following:
plotTree.singletons to permit multifurcations.
(4) A new version of the
biplot method for objects of class
"phyl.pca" to permit choice in the PC axes to be plotted
(5) A kindly user-supplied
(6) A fix in how the environmental variable
"last_plot.phylo" is created
(7) Updates to a wide range of phytools plotting functions to permit smoother plotting and animation.
Finally, (8) major update to
plotTree.wBars to permit tip labels to be
In addition to this non-comprehensive list of phytools updates, I also made many changes and additions to the phytools manual pages for the present CRAN release.
There were a few different functions described on the phytools blog that have not been added to this package update but may feature in a future version of phytools.
(1) A function to identify the youngest node on the tree with N or more descendant tips (here).
(3) A function to convert a phylogeny with node labels to a taxonomy (here).
Here is a previously posted video showing use of the phytools interactive tree pruner,