Bootstrapping Phylogenetic Trees: Theory and Methods

Bootstrapping Phylogenetic Trees: Theory and Methods

This is a survey of the use of the bootstrap in the area of systematic and evolutionary biology. I present the current usage by biologists of the bootstrap as a tool both for making inferences and for evaluating robustness, and propose a framework for thinking about these problems in terms of mathematical statistics.

Coalescent methods for estimating phylogenetic trees.

We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to...

Development of New Methods for Inferring and Evaluating Phylogenetic Trees

Matchings and phylogenetic trees.

This paper presents a natural coordinate system for phylogenetic trees using a correspondence with the set of perfect matchings in the complete graph. This correspondence produces a distance between phylogenetic trees, and a way of enumerating all trees in a minimal step order. It is useful in randomized algorithms because it enables moves on the space of trees that make random optimization str...

Operads and phylogenetic trees

We construct an operad Phyl whose operations are the edge-labelled trees used in phylogenetics. This operad is the coproduct of Com, the operad for commutative semigroups, and [0,∞), the operad with unary operations corresponding to nonnegative real numbers, where composition is addition. We show that there is a homeomorphism between the space of n-ary operations of Phyl and Tn × [0,∞)n+1, wher...