Abstract Motivation Phylogenetic analysis like Bayesian MCMC or bootstrapping result in a
collection of trees. Trees are discrete objects and it is generally difficult to get a mental grip …

Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly,
researchers need to visualize large trees and compare multiple large trees inferred for the …

Motivation: Bayesian analysis through programs like BEAST (Drummond and Rumbaut,)
and MrBayes (Huelsenbeck et al.,) provides a powerful method for reconstruction of …

Background Today it is common to apply multiple potentially conflicting data sources to a
given phylogenetic problem. At the same time, several different inference techniques are …

Phylogenetic trees illustrate evolutionary relationships between taxa or genes. Tree figures
are crucial when presenting results and data, and by creating clear and effective plots …

Toytree is a lightweight Python library for programmatically visualizing and manipulating tree‐
based data structures. It implements a minimalist design aesthetic and modern plotting …

Background Research in evolution requires software for visualizing and editing phylogenetic
trees, for increasingly very large datasets, such as arise in expression analysis or …

Phylogenetic analyzes under the Maximum-Likelihood (ML) model are time and resource
intensive. To adequately capture the vastness of tree space, one needs to infer multiple …

If predictions for species extinctions hold, then the 'tree of life'today may be quite different to
that in (say) 100 years. We describe a technique to quantify how much each species is likely …

Phylogenetic analyses often produce large numbers of trees. Mapping trees' distribution in
“tree space” can illuminate the behavior and performance of search strategies, reveal …