Thursday, March 15, 2012

Online primer of phylogenetic networks

I have long felt the need for a simple introduction to networks for those people who know something about phylogenetic trees and would like to find out what this "network business" is all about.

So, I have attempted to create such a thing by writing an online primer.

It takes a toy dataset (real data for two genes from five species) and leads the reader step by step through the construction of various trees and networks, including a parsimony tree, a median network, a recombination network and a hybridization network. So, mathematically it tries to explain the relationship between these different ways of viewing the same dataset. Biologically, it considers the possible conflicts between characters within a gene as well as between genes, and what this might mean for phylogenetic analysis.

The primer can be read online, or downloaded as a PDF file (for printing) or an ePub file (for reading on small screens).

Any constructive feedback will be gratefully received.


  1. As a watercolor artist I was once requested to paint a phylogeny network and subsequently fell in love with the figures. I recently decided to return to the subject matter and wanted a better understanding of how they are generated. I simply wanted to let you know how much I greatly appreciated your online primer. Thanks tremendously!