Thursday, December 10, 2015

New version of phytools on CRAN. Check it out!

There is a new version of phytools on CRAN.

Here are some of the updates since the previous version:

  1. A bug fix in make.simmap for Q="mcmc".

  2. A new function fastDist to compute the patristic distance between two species.

  3. A minor bug fix in plotSimmap when the edge order of the input tree is "pruningwise".

  4. The addition of a scale bar for the plot.cophylo S3 method.

  5. A total re-write of the internally used function phyloDesign. (It's also now in the name space.)

  6. A small update to the phytools function to fix malconformed trees (untangle).

  7. Update to cophylo for trees without edge lengths (here).

  8. Functionality to add node, edge, and tip labels to a plotted object of class "cophylo".

  9. New functionality in plotTree.wBars for user control of the bar colors (here).

  10. New interactive modes for the phytools functions bind.tip and reroot.

  11. Update to to permit right- facing trees.

  12. Update to to permit use with nodelabels, tiplabels, and edgelabels from ape (here).

  13. An important update for describe.simmap (and thus the S3 summary method for objects of class "multiSimmap") when trees have potentially incongruent topologies.

  14. A new function to simulate a stochastic species-level tree from a genus backbone tree.

  15. An update to contMap to permit user-supplied node states.

  16. A new feature in fastAnc to permit some node states to be fixed.

  17. A new function for computing the relative frequency of different types of state changes along edges in a set of stochastic-mapped trees.

  18. A function to comute the matrix-representation of a tree for mrp.supertree - although it can also be used on it's own (here).

  19. A variety of bug fixes in phenogram, fastAnc, fitMk, and rerootingMethod, detailed here.

  20. And, finally, separate user control of edge & legend line widths in plot.contMap.

Along with some other changes & bug fixes. Check it out!


  1. I can't use phytools with the latest R vesion (3.2.3), because phytools requires package ‘Biostrings’, which is not available for R version 3.2.3. :(

    1. Hi Andrey.

      Yes, this is an issue with the dependency on phangorn. Klaus Schliep, the author & maintainer of phangorn, posted a solution here. Let us know if that works.

      All the best, Liam

    2. Hi Liam,

      Thank you for the swift reply and the link! Now it works!!!

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