The updated Primer of Phylogenetic Networks

In an earlier post I reported on the creation of an Online Primer of Phylogenetic Networks, which is intended as a simple introduction to networks for those people who already know something about phylogenetic trees. This includes three animations (animated GIF files).

This primer has now been updated with explanations of the construction of Reduced Median Networks, Median-Joining Networks and Minimum-Spanning Trees.

So, the primer now includes:

• Median Networks
• Reduced Median Networks
• Median-Joining Networks
• Recombination Networks
• Hybridization Networks
• Parsimony Trees
• Minimum-Spanning Trees

These are all related to each other, and can be easily explained by looking at the distribution of the characters in a parsimony context. With the exception of NeighborNet, this covers the networks that most commonly appear in the literature.

Any constructive feedback will be gratefully received.

The all-dancing Primer of Phylogenetic Networks

In an earlier post I reported on the creation of an Online Primer of Phylogenetic Networks, which is intended as a simple introduction to networks for those people who already know something about phylogenetic trees. The primer can be read online, or downloaded as a PDF file (for printing) or as an ePub file (for reading on small screens).

Here, I note that the online version of the primer has now been updated with three animations (animated GIF files). These illustrate:

1. the creation of a Median Network from character data;
2. the creation of a Parsimony Tree from a Median Network, and
3. the creation of a Recombination Network from a Median Network.

Any constructive feedback will be gratefully received.

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.