The Triples Distance for Rooted Bifurcating Phylogenetic Trees

Critchlow, Douglas E.; Pearl, Dennis K.; Qian, Chunlin

doi:10.2307/2413567

Cited by 35 publications

(53 citation statements)

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“…In order to quantify the reconstruction accuracy, we employed a triples distance (Critchlow et al 1996) approach (see Supplemental Fig. S18) and calculated the percentage of triples in the reconstructed tree that match the topology of the real tree.…”

Section: Cell Lineage Tree Of Ex Vivo Grown Cancer Cellsmentioning

confidence: 99%

A generic, cost-effective, and scalable cell lineage analysis platform

et al. 2016

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Advances in single-cell genomics enable commensurate improvements in methods for uncovering lineage relations among individual cells. Current sequencing-based methods for cell lineage analysis depend on low-resolution bulk analysis or rely on extensive single-cell sequencing, which is not scalable and could be biased by functional dependencies. Here we show an integrated biochemical-computational platform for generic single-cell lineage analysis that is retrospective, cost-effective, and scalable. It consists of a biochemical-computational pipeline that inputs individual cells, produces targeted single-cell sequencing data, and uses it to generate a lineage tree of the input cells. We validated the platform by applying it to cells sampled from an ex vivo grown tree and analyzed its feasibility landscape by computer simulations. We conclude that the platform may serve as a generic tool for lineage analysis and thus pave the way toward large-scale human cell lineage discovery.

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Section: Cell Lineage Tree Of Ex Vivo Grown Cancer Cellsmentioning

confidence: 99%

A generic, cost-effective, and scalable cell lineage analysis platform

et al. 2016

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“…nearest neighbor interchange metric [44], the subtree transfer distance [1], the triplet metric [10], and the nodal distance [6]. But, to our knowledge, beside the natural extension of the Robinson-Foulds metric to regular networks (whose nodes are singled out by their sets of descendant leaves) [4], only one metric (up to small variations) for phylogenetic networks has been proposed so far.…”

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confidence: 99%

Comparison of Tree-Child Phylogenetic Networks

Cardona

Rosselló

Valiente

2009

IEEE/ACM Trans. Comput. Biol. and Bioinf.

171

224

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Abstract-Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of nontreelike evolutionary events, like recombination, hybridization, or lateral gene transfer. While much progress has been made to find practical algorithms for reconstructing a phylogenetic network from a set of sequences, all attempts to endorse a class of phylogenetic networks (strictly extending the class of phylogenetic trees) with a well-founded distance measure have, to the best of our knowledge and with the only exception of the bipartition distance on regular networks, failed so far. In this paper, we present and study a new meaningful class of phylogenetic networks, called tree-child phylogenetic networks, and we provide an injective representation of these networks as multisets of vectors of natural numbers, their path multiplicity vectors. We then use this representation to define a distance on this class that extends the well-known Robinson-Foulds distance for phylogenetic trees and to give an alignment method for pairs of networks in this class. Simple polynomial algorithms for reconstructing a tree-child phylogenetic network from its path multiplicity vectors, for computing the distance between two tree-child phylogenetic networks and for aligning a pair of tree-child phylogenetic networks, are provided. They have been implemented as a Perl package and a Java applet, which can be found at

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“…The most popular include the nearest-neighbor interchange (NNI) distance (Robinson 1971;Moore, Goodman, and Barnabas 1973), subtree-transfer distance (Hein 1993), triples distance (Critchlow, Pearl, and Qian 1996), and the branch score metric (Kuhner and Felsenstein 1994). Subtree transfer is most appropriate when considering such events as recombination or gene conversion and the triples distance is not uniquely de ned for unrooted trees.…”

Section: The Branch Score Metric On Evolutionary Historiesmentioning

confidence: 99%

Evolutionary Similarity Among Genes

Suchard

Weiss

Sinsheimer

et al. 2003

Journal of the American Statistical Association

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An evolutionary history of a set of organisms is a family tree, or topology, with branches of various lengths between vertices that describe how closely the organisms are related to each other. We consider the K evolutionary histories of K genes from a set of N organisms. Evolutionary similarity (ES) occurs when the branching patterns and relative branch lengths in the K evolutionary histories of the genes are the same or nearly the same across the set of organisms. Evolutionary similarity indicates similarity of evolutionary pressures acting on these genes. Current likelihood approaches identify ES conditional on a given topology. For a variety of reasons, different genes may support different topologies when t independently. We use Bayesian models and reversible-jump Markov chain Monte Carlo to jointly infer topology and branch lengths for multiple genes simultaneously. We test for ES using Bayes factors, conditionally on a consistent topology over the multiple genes, where the topology is either known or unknown. We relax the single topology assumption by employing a dissimilarity measure between evolutionary histories and testing for ES using both prior and posterior predictive p values. We apply our methodology to three genes (DAX1, SOX9, and SRY) believed to be involved in sex determination in primates. We nd support in the data for ES between DAX1 and SRY, but not SOX9. These results are consistent with the hypothesized biological roles of these genes.

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The Triples Distance for Rooted Bifurcating Phylogenetic Trees

Cited by 35 publications

References 0 publications

A generic, cost-effective, and scalable cell lineage analysis platform

A generic, cost-effective, and scalable cell lineage analysis platform

Comparison of Tree-Child Phylogenetic Networks

Evolutionary Similarity Among Genes

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