Bioinformatics with Python Cookbook - Second Edition

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Tree and graph visualization is a complex topic; we will revisit this subject in Chapter 10, Other Topics in Bioinformatics, when we interface with Cytoscape. One interesting free software alternative (Java-based) for graph visualization is Gephi (http://gephi.github.io/). If you want to know more about the algorithms for rendering trees and graphs, check the Wikipedia page at http://en.wikipedia.org/wiki/Graph_drawing for an introduction to this fascinating topic.

Be careful not to trade style for substance, though. For example, the previous edition of this book had a pretty rendering of a phylogenetic tree using a graph-rendering library. While it was clearly the most beautiful image in that chapter, it was misleading in ...