bielcardona/PhyloNetworks — pull request #4 by dscharles (2012-04-03 11:40:51+00:00)
Title: PhyloTree methods

Added some methods in PhyloTree:

* LCA
* nodal_matrix
* cluster
* depth

Some expectacular improvements over PhyloNetwork implementation:

```python
taxa = range(100)
taxa = map(str, taxa)

net = random_yule_tree(taxa)
tree = PhyloTree(eNewick=net.eNewick())

net.nodal_matrix() # around 6.5 s.
tree.nodal_matrix() # ~ 0.6 s.
```
---
```python
net = random_tree_nobin_nt_global(taxa, id_offset=0)
tree = PhyloTree(eNewick=net.eNewick())

net.nodal_matrix() # ~ 4.4 s.
tree.nodal_matrix() # ~ 0.5 s.
```