How To Make A Phylogeny In R

R Programming

Today, I’m excited to share with you the process of creating a phylogeny using R, a powerful statistical programming language that is widely used in bioinformatics and biological research. Phylogeny, or evolutionary history, of species has always fascinated me, and being able to visualize it using R is both rewarding and insightful.

Understanding Phylogeny

Before diving into the R code, it’s essential to understand the concept of phylogeny. Phylogenetic trees are diagrams used to show the evolutionary relationships among various biological species. These trees are essential in understanding the evolutionary history of organisms and are widely used in fields such as evolutionary biology, ecology, and conservation biology.

Getting Started with R

To begin, ensure you have R and RStudio installed on your system. RStudio provides a user-friendly interface for writing and executing R code, making the process more efficient and organized.

Once you have R and RStudio set up, you’ll need to install the necessary packages for phylogenetic analysis. The ‘ape’ package is a popular choice for creating and manipulating phylogenetic trees in R. You can install it using the following command:


Importing Data

Next, you’ll need to import your sequence data into R. This data typically consists of DNA or protein sequences that will be used to build the phylogenetic tree. You can read in your sequence data from a file using functions like read.dna() or from the ‘ape’ package.

Building the Phylogeny

Once your data is loaded into R, you can start building your phylogenetic tree. The most common method for creating a phylogeny is through the use of algorithms like neighbor-joining or maximum likelihood. The ‘ape’ package provides functions such as nj() and mlik() for this purpose.

Visualizing the Tree

After building the phylogenetic tree, you’ll want to visualize and customize its appearance. The ‘ape’ package offers tools for plotting and annotating trees. You can use functions like plot.phylo() and axisPhylo() to create publication-quality visualizations of your phylogeny.

Adding Personal Touches

One of the aspects I enjoy most about working with phylogenies in R is the ability to add personal touches to the visualizations. Whether it’s customizing the color scheme, adding labels, or altering the tree layout, R provides the flexibility to make the phylogeny reflect your unique style and preferences.


Creating a phylogeny in R is a rewarding and insightful process that allows for a deeper understanding of evolutionary relationships among species. By leveraging the capabilities of R and the ‘ape’ package, you can not only build phylogenetic trees but also personalize and refine the visualizations to suit your specific needs and preferences. I encourage you to explore the world of phylogenetic analysis in R and uncover the fascinating stories hidden within evolutionary trees.