Results 71 to 80 of about 489,513 (135)
Community Phylogenetics: Assessing Tree Reconstruction Methods and the Utility of DNA Barcodes.
PLoS ONE, 2015 Studies examining phylogenetic community structure have become increasingly prevalent, yet little attention has been given to the influence of the input phylogeny on metrics that describe phylogenetic patterns of co-occurrence.
Elizabeth E Boyle, Sarah J Adamowicz
doaj +1 more source
On Tree Based Phylogenetic Networks [PDF]
arXiv, 2015 A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all tree based. In this work, we present a simply necessary and sufficient condition for tree-based networks and prove ...
arxiv
Trinets encode tree-child and level-2 phylogenetic networks [PDF]
arXiv, 2012 Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to develop methods to construct rooted phylogenetic networks from ...
arxiv
Consistency of the Neighbor-Net Algorithm
Algorithms for Molecular Biology, 2007 Background Neighbor-Net is a novel method for phylogenetic analysis that is currently being widely used in areas such as virology, bacteriology, and plant evolution.
Moulton Vincent +2 more
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The isometry group of phylogenetic tree space is $S_n$ [PDF]
arXiv, 2019 A phylogenetic tree is an acyclic graph with distinctly labeled leaves, whose internal edges have a positive weight. Given a set of n leaves, the collection of all phylogenetic trees with this leaf set can be assembled into a metric cube complex known as phylogenetic tree space, or Billera-Holmes-Vogtmann tree space. In this largely combinatorial paper,
arxiv
Nonbinary tree-based phylogenetic networks [PDF]
arXiv, 2016 Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can for example represent gene transfer events.
arxiv
Syntactic Phylogenetic Trees [PDF]
arXiv, 2016 In this paper we identify several serious problems that arise in the use of syntactic data from the SSWL database for the purpose of computational phylogenetic reconstruction. We show that the most naive approach fails to produce reliable linguistic phylogenetic trees. We identify some of the sources of the observed problems and we discuss how they may
arxiv
Reliable estimation of tree branch lengths using deep neural networks.
PLoS Computational BiologyA phylogenetic tree represents hypothesized evolutionary history for a set of taxa. Besides the branching patterns (i.e., tree topology), phylogenies contain information about the evolutionary distances (i.e. branch lengths) between all taxa in the tree,
Anton Suvorov, Daniel R Schrider
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Taxonomic colouring of phylogenetic trees of protein sequences
BMC Bioinformatics, 2006 Background Phylogenetic analyses of protein families are used to define the evolutionary relationships between homologous proteins. The interpretation of protein-sequence phylogenetic trees requires the examination of the taxonomic properties of the ...
Andrade-Navarro Miguel A +2 more
doaj +1 more source
Bridging the gap between rooted and unrooted phylogenetic networks [PDF]
arXiv, 2015 The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also allowing cycles and have been introduced in rooted and unrooted form. In contrast to phylogenetic trees, however,
arxiv