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Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from minor variations of the input data, trees called replicates. BS is used with all phylogenetic reconstruction approaches, but we focus here on one of the most popular, maximum likelihood (ML). Because… (More)

The Robinson-Foulds (RF) metric is the measure most widely used in comparing phylogenetic trees; it can be computed in linear time using Day's algorithm. When faced with the need to compare large numbers of large trees, however, even linear time becomes prohibitive. We present a randomized approximation scheme that provides, in sublinear time and with high… (More)

Many of the steps in phylogenetic reconstruction can be confounded by " rogue " taxa, taxa that cannot be placed with assurance anywhere within the tree—whose location within the tree, in fact, varies with almost any choice of algorithm or parameters. Phylogenetic consensus methods, in particular, are known to suffer from this problem. In this paper we… (More)

A Maximum Agreement SubTree (MAST) is a largest subtree common to a set of trees and serves as a summary of common substructure in the trees. A single MAST can be misleading, however, since there can be an exponential number of MASTs, and two MASTs for the same tree set do not even necessarily share any leaves. In this paper, we introduce the notion of the… (More)

Gene rearrangements have been used successfully in phylogenetic reconstruction and comparative genomics, but usually under the assumption that all genomes have the same gene content and that no gene is duplicated. While these assumptions allow one to work with organellar genomes, they are too restrictive for nuclear genomes. The main challenge in handling… (More)

Many of the steps in phylogenetic reconstruction can be confounded by "rogue” taxa—taxa that cannot be placed with assurance anywhere within the tree, indeed, whose location within the tree varies with almost any choice of algorithm or parameters. Phylogenetic consensus methods, in particular, are known to suffer from this problem. In this… (More)

The Robinson-Foulds (RF) metric is the measure most widely used in comparing phylogenetic trees; it can be computed in linear time using Day's algorithm. When faced with the need to compare large numbers of large trees, however, even linear time becomes prohibitive. We present a randomized approximation scheme that provides, with high probability, a (1 + ε)… (More)

The field of bioinformatics is witnessing a rapid and overwhelming accumulation of molecular sequence data, predominantly driven by novel wet-lab sequencing techniques. This trend poses scalability challenges for tool developers. In the field of phylogenetic inference (reconstruction of evolutionary trees from molecular sequence data), scalability is… (More)

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