Phylogenetic trees

Phylogenetics describes the taxonomical classification of organisms based on their evolutionary history i.e. their phylogeny. Phylogenetics is therefore an integral part of the science of systematics that aims to establish the phylogeny of organisms based on their characteristics. Furthermore, phylogenetics is central to evolutionary biology as a whole as it is the condensation of the overall paradigm of how life arose and developed on earth. The focus of this module is the reconstruction and visualization of phylogenetic trees. Phylogenetic trees illustrate the inferred evolutionary history of a set of organisms, and makes it possible to e.g. identify groups of closely related organisms and observe clustering of organisms with common traits. See 13.1.1 for a more detailed introduction to phylogenetic trees.

The viewer for visualizing and working with phylogenetic trees allows the user to create high-quality, publication-ready figures of phylogenetic trees. Large trees can be explored in two alternative tree layouts; circular and radial.

Below is an overview of the main features of the phylogenetic tree editor. Further details can be found in the subsequent sections.

Main features of the phylogenetic tree editor:

For a given set of aligned sequences (see Create an alignment) it is possible to infer their evolutionary relationships using a distance based method to generate a phylogenetic tree (see Bioinformatics explained). Create Tree (Image tree) is a tool that uses distance estimates computed from multiple alignments to generate phylogenetic trees. The user can select whether to use Jukes-Cantor distance correction or Kimura distance correction (Kimura 80 for nucleotides/Kimura protein for proteins) in combination with either the neighbor joining or UPGMA method (see Distance-based methods).


Subsections