I just posted a new alpha version of "phytools," version 0.0-6, to my website here.
Here is a list of updates or additions from the previous version:
1. New function map.overlap() that computes the fractional overlap between two stochastically mapped phylogenies (described here).
2. More robust version of brownie.lite() that avoids the problem of "false convergence" in the multi-rate model (described here).
3. New and improved versions of plotSimmap() and plotTree(). These versions have more plotting options including the option to plot without tip labels.
4. Fixed lineage-through-time function ltt(). Bug & fix described here & here, respectively.
Please check it out! Feedback welcome.