I’m working on a toy model of community assembly in Python, and I thought it would be cool to have an easy way to keep track of the phylogeny. To do so, I’ve conceived two classes for the easy handling of phylogenetic structure. They are available on GitHub in the PyCoPhy repository (Python Community Phylogenetics), and check also the code page.

The general idea behind them is quite easy to understand. A phylogenetic tree is a list of branchings. A branching is the junction of two objects, which I called left and right. Each of these objects can be an identifier (i.e. a leaf of the tree), or a reference to another branching (i.e. a node). It’s as complicated as it gets.

Once PyCoPhy is loaded, to create a new tree with a species called ancestor, just type:

iTree = PhyloTree('ancestor')
print iTree

The output of this command should be (root, ancestor). The root is created by default to ensure that the most basal node is a branching. The interesting thing is that it’s now relatively easy to add and remove species. The PhyloTree class has the speciate method, who takes two arguments: the name of the ancestor, and the name of the daughter species. Calling it will go through the tree, and replace the ancestor by the (ancestor, daughter species) branching. Let’s try with:

iTree = PhyloTree('0')
iTree.speciate('0','0_0')
print iTree

which results in the following tree: (root,(0,0_0)). And I know this is not the way speciation works, so there is also a split method, which will replace one ancestral species by two new species:

iTree = PhyloTree('0')
iTree.split('0','1','2')
print iTree

will result in (root,(2,1)). This is all made possible by the extinct method, by the way, which will remove from the tree the species whose name is given in argument:

iTree = PhyloTree('0')
iTree.split('0','1','2')
iTree.extinct('2')
print iTree

will result in (root,1).

Although these classes are really basic at the moment, they allow me to easily keep track of who is related to who in my simulations. I’ll most likely add a way to keep track of branch lenghts at some point in the near future.