Methods for automatic reference trees and multilevel phylogenetic placement

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...

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.

Development of New Methods for Inferring and Evaluating Phylogenetic Trees

4-PLACEMENT OF ROOTED TREES

A tree T of order n is called k-placement if there are k edge-disjoint copies of T into K_{n}. In this paper we prove some results about 4-placement of rooted trees.

Automatic genome-wide reconstruction of phylogenetic gene trees

UNLABELLED Gene duplication and divergence is a major evolutionary force. Despite the growing number of fully sequenced genomes, methods for investigating these events on a genome-wide scale are still in their infancy. Here, we present SYNERGY, a novel and scalable algorithm that uses sequence similarity and a given species phylogeny to reconstruct the underlying evolutionary history of all gen...