What is Subtree Pruning and Regrafting (SPR)?
We’ve previously discussed the sheer size of tree space. As the number of taxa (or leaves) increases, the number of Continue Reading …
Introduction to Homologs, Orthologs and Paralogs
What is a Homolog? Homolog is a broad term that describes any gene that shares a common evolutionary ancestor with Continue Reading …
Introduction to Sequence Substitution Models
What is a substitution? A substitution is a type of mutation where a single nucleotide base (A,C, G, T) is Continue Reading …
Introduction to the Molecular Clock
In this post we’ll introduce a few key ideas relating to the molecular clock. What is the Molecular Clock? The Continue Reading …
Coalescent trees and Bugs in a box
Imagine tracing a tree diagram backwards in time, from the tips all the way back to its root. At each Continue Reading …
The Neighbour-Joining algorithm: Ties and Matrix Order
Following on from the previous post Foundations of phylogenetics we’ll next explore how ties and matrix order can influence the Continue Reading …
Foundations of phylogenetics
For many years it was believed that patterns of evolution are tree-like and sometimes they are! We now know that Continue Reading …
Clustering to Reveal Hidden Traits: Using Neighbour-Joining Trees
Before we dive into the theory behind the Neighbour-Joining algorithm I wanted to do a simple conceptual exercise to highlight Continue Reading …
Decoding phylogenetic tree shapes
Phylogenetic trees can tell us about more than just the hierarchical order of our dataset. Taken together the position of Continue Reading …
What is a rooted tree?
Rooted trees A rooted tree is a tree diagram where the branches are ordered descending from a ‘root point’ The Continue Reading …