Sketch, capture and layout phylogenies

Phylogenetic trees and networks play a central role in biology, bioinformatics, and mathematical biology, and producing clear, informative visualizations of them is an important task. We present new algorithms for visualizing rooted phylogenetic networks in either a "combining" or "transfer" view, in both cladogram and phylogram style. In addition, we introduce a layout algorithm that aims to improve clarity by minimizing the total reticulate displacement of reticulate edges. To address the common issue that biological publications often omit machine-readable representations of depicted trees and networks, we also provide an image-based algorithm that assists in extracting their topology from figures. All algorithms are implemented in our new open source PhyloSketch app.