Maximum Likelihood vs Bayesian Phylogenetics
We’ve touched on how we must navigate an enormous landscape through tree space using phylogenetic algorithms. We’ll now explore the Continue Reading …
What is a k-mer?
A k-mer is a substring of a biological sequence with length K, where K can be any number. If you 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 …
Building and running a Docker container
In this post we’ll go through how to build and run a docker container! For our example we will use Continue Reading …
Containerisation for research software
Containerisation is the process of packaging software with its dependencies (eg. tools, libraries, configurations) into a container. Using containerisation improves Continue Reading …
Using alignment viewers: An Introduction with Aliview
When we are working on individual genes or proteins, or we just want to take a closer look at sequences, Continue Reading …
Getting started with population analysis in R
A population is another word for a group of individuals. For population studies we often want to analyse groups of Continue Reading …
Introduction to sequence analysis in R
In this post we will look at how to read, write and analyse fasta sequences in R using the ape, Continue Reading …