Book contents
- Frontmatter
- Contents
- Preface
- Part I Introduction
- Part II Theory
- Part III Algorithms and applications
- 7 Phylogenetic networks from splits
- 8 Phylogenetic networks from clusters
- 9 Phylogenetic networks from sequences
- 10 Phylogenetic networks from distances
- 11 Phylogenetic networks from trees
- 12 Phylogenetic networks from triples or quartets
- 13 Drawing phylogenetic networks
- 14 Software
- Glossary
- References
- Index
13 - Drawing phylogenetic networks
from Part III - Algorithms and applications
Published online by Cambridge University Press: 05 August 2011
- Frontmatter
- Contents
- Preface
- Part I Introduction
- Part II Theory
- Part III Algorithms and applications
- 7 Phylogenetic networks from splits
- 8 Phylogenetic networks from clusters
- 9 Phylogenetic networks from sequences
- 10 Phylogenetic networks from distances
- 11 Phylogenetic networks from trees
- 12 Phylogenetic networks from triples or quartets
- 13 Drawing phylogenetic networks
- 14 Software
- Glossary
- References
- Index
Summary
The algorithms presented in the previous chapters compute a phylogenetic tree or network as a labeled graph, possibly with edge lengths. In this chapter, we discuss the problem of assigning coordinates to the nodes (and sometimes also to points along the edges) of a given phylogenetic tree or network so that it can be drawn by a computer program. The results presented here are based on [62, 77, 124].
Overview
Figure 13.1 shows the relationships between some of the main concepts introduced in this chapter. The focus of this chapter is on how to draw phylogenetic trees and networks.
A rooted network or tree can be depicted either as a phylogram, in which the edges are drawn to scale and thus represent, for example, distances or the number of mutations along an edge, or as a cladogram, which aims at representing only the topology of the network. Both types of drawings come in a number of different variants, including triangular, rectangular and circular diagrams. We need to distinguish between a combining view and a transfer view of a rooted phylogenetic network. In the former, all in-edges of a reticulate node are drawn as reticulate edges, whereas as in the latter one in-edge is drawn as a tree edge and all other in-edges are drawn as directed edges that indicate transfer events, see Section 13.6.
An unrooted network or tree is usually drawn to scale as a radial diagram.
We first discuss algorithms for drawing trees and then modify these so as to obtain algorithms for drawing phylogenetic networks.
- Type
- Chapter
- Information
- Phylogenetic NetworksConcepts, Algorithms and Applications, pp. 312 - 331Publisher: Cambridge University PressPrint publication year: 2010