blab/augur — pull request #5 by rneher (2014-09-28 18:38:22+00:00)
Title: Richard xps13

Added tree_LBI.py which calculates the local branching index (LBI) for each node of the tree. The LBI is essentially the tree length surrounding a node exponentially discounted with distance from the node. It is efficiently calculated by a 2pass algorithm on the tree. Its only parameter is the time scale of the exponential discounting, which we be default choose to be 16times smaller than the average pairwise distance of nodes sampled at the same time. tree_LBI.py contains a set of function that calculate this average T2 for subsets of nodes sampled in one year.