Clock trees implementation

[PhyloStar]

Clock trees implementation is something to think about.

Drummond et al. 2002 (http://www.genetics.org/content/161/3/1307.long) is the best paper that has MCMC moves close to what I implemented in this package.

• Birth-death trees with incomplete sampling and extant languages. Yang and Rannala is the reference when using the tree probability as the prior.
• Uniform tree prior from Ronquist et al. (2012) is the paper for uniform prior.
• Yang's chapter on coalescent process is the book chapter which presents the theory behind coalescent prior that is easy to simulate using a exponential waiting time. I will add some code to simulate.
• Strict clock involves adding a single parameter that links the linguistic branch lengths to geographical timescale.

How to generate a time tree is the question? As of now the trees are rooted. However, a time tree would have all the tips at same level. That will introduce extra complications that might need to be handled. Any ideas on how to sample a starting tree are welcome.