Review Paper: The Shape of Phylogenetic Treespace

  title={Review Paper: The Shape of Phylogenetic Treespace},
  author={Katherine St John},
  journal={Systematic Biology},
  pages={e83 - e94}
Trees are a canonical structure for representing evolutionary histories. Many popular criteria used to infer optimal trees are computationally hard, and the number of possible tree shapes grows super-exponentially in the number of taxa. The underlying structure of the spaces of trees yields rich insights that can improve the search for optimal trees, both in accuracy and in running time, and the analysis and visualization of results. We review the past work on analyzing and comparing trees by… 

Tropical Geometry of Phylogenetic Tree Space: A Statistical Perspective

A novel framework to study sets of phylogenetic trees based on tropical geometry is proposed and studied, which exhibits analytic, geometric, and topological properties that are desirable for theoretical studies in probability and statistics, as well as increased computational efficiency over the current state-of-the-art.

Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees

This paper shows that the computational efficiency of Bayesian inference under the multispecies coalescent can be improved in practice by restricting the space of the gene trees explored during the random walk, without sacrificing accuracy as measured by various metrics.

ENJ algorithm can construct triple phylogenetic trees

Computational Phylogenetics: An Introduction to Designing Methods for Phylogeny Estimation

The author provides key analytical techniques to prove theoretical properties about methods, as well as addressing performance in practice for methods for estimating trees, in the broad and exciting field of computational phylogenetics.

Mean and Variance of Phylogenetic Trees.

The Fréchet mean and variance are more theoretically justified, and more robust, than previous estimates of this type, and can be estimated reasonably efficiently, providing a foundation for building more advanced statistical methods and leading to applications such as mean hypothesis testing and outlier detection.

Rearrangement operations on unrooted phylogenetic networks

This work proves connectedness and asymptotic bounds on the diameters of spaces of different classes of phylogenetic networks, including tree-based and level-$k$ networks and shows that computing the TBR-distance and the PR-distance of two phylogenetic Networks is NP-hard.

The agreement distance of rooted phylogenetic networks

Maximum agreement graphs are introduced as a generalisations of maximum agreement forests for phylogenetic networks and it is shown that it still provides constant-factor bounds on the TBR-distance.

Tree Evaluation and Robustness Testing

Statistical approaches to viral phylodynamics

A pipeline for a typical phylodynamic analysis which includes convergence diagnostics for continuous parameters and in phylogenetic space, extending existing methods to deal with large time-calibrated phylogenies and investigating different representations of phylogeneticspace through multi-dimensional scaling (MDS) or univariate distributions of distances.

Effective Online Bayesian Phylogenetics via Sequential Monte Carlo with Guided Proposals

It is shown that proposing new phylogenies with a density similar to the Bayesian prior suffers from poor performance, and ‘guided’ proposals are developed that better match the proposal density to the posterior.



Geometry of the Space of Phylogenetic Trees

We consider a continuous space which models the set of all phylogenetic trees having a fixed set of leaves. This space has a natural metric of nonpositive curvature, giving a way of measuring

On the Neighborhoods of Trees

An exact expression for the size of the TBR (tree bisection and reconnection) neighborhood is presented, thus answering a question first posed by Allen and Steel .

Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees

  • John ChakerianS. Holmes
  • Computer Science
    Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America
  • 2012
The implementation of the geometric distance between trees developed by Billera, Holmes, and Vogtmann (2001) is described, equally applicable to phylogenetic trees and hierarchical clustering trees, and some of the applications in evaluating tree estimates are shown.

Terraces in Phylogenetic Tree Space

Previously unknown structure in the landscape of solutions to the tree reconstruction problem is described, comprising sometimes vast “terraces” of trees with identical quality, arranged on islands of phylogenetically similar trees.

A regular decomposition of the edge-product space of phylogenetic trees

Slicing hyperdimensional oranges: the geometry of phylogenetic estimation.

  • J. Kim
  • Biology
    Molecular phylogenetics and evolution
  • 2000
A new view of phylogenetic estimation is presented where data sets, tree evolution models, and estimation methods are placed in a common geometric framework that allows intuitive understanding of various complex properties of the phylogeneticestimation problem structure.

Efficient algorithms for inferring evolutionary trees

These problems of inferring the evolutionary history of n objects, either from present characters of the objects or from several partial estimates of their evolutionary history, can be solved by graph theoretic methods in linear time, which is time optimal, and which is a significant improvement over existing methods.

Large-scale analysis of phylogenetic search behavior.

By analyzing all trees from search, this work finds that, as the search algorithm climbs the hill to local optima, the trees in the neighborhood surrounding the current solution improve as well, and the search is quite robust to a small number of randomly selected neighbors.

An Algorithm for Constructing Principal Geodesics in Phylogenetic Treespace

  • T. Nye
  • Environmental Science
    IEEE/ACM Transactions on Computational Biology and Bioinformatics
  • 2014
A stochastic algorithm for constructing a principal geodesic or line through treespace which is analogous to the first principal component in standard principal components analysis, though convergence to locally optimal geodesics is possible.