Wednesday, April 29, 2015

New version of phytools (phytools 0.4-56) now on CRAN

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:

(1) A bug fix in plotTree.singletons to permit multifurcations.

(2) Multiple fixes to the function reroot for trees with node labels (1, 2, 3).

(3) A new interactive tree plotter (collapseTree) to collapse & expand a fan-style phylogeny (1, 2, 3).

(4) A new version of the biplot method for objects of class "phyl.pca" to permit choice in the PC axes to be plotted (here).

(5) A kindly user-supplied bug fix for fastAnc.

(6) A fix in how the environmental variable "last_plot.phylo" is created by plotSimmap (here).

(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 plotted (here).

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.

For example:

(1) A function to identify the youngest node on the tree with N or more descendant tips (here).

(2) A function to simulate random branch lengths under a pure-birth (Yule process) conditioned on a user-supplied tree topology (1, also see 2).

(3) A function to convert a phylogeny with node labels to a taxonomy (here).

Finally, (4) a function to split a plotted tree across multiple plotting devices or pages (1, 2).

Obviously, the latest version of phytools can be obtained from as well as from the phytools CRAN page.

Here is a previously posted video showing use of the phytools interactive tree pruner, collapseTree:

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