Results 21 to 30 of about 300,530 (260)
Robust information from phylogenetic trees? [PDF]
, 2010 Traditional information criteria approaches can lead to misleading model choice in comparative phylogenetics. I present both these weaknesses and a more robust comparison by likelihood ratio.
Carl Boettiger
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Rearrangement operations on unrooted phylogenetic networks
Theory and Applications of Graphs, 2019 Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree prune and ...
Remie Janssen, Jonathan Klawitter
doaj +1 more source
Cophenetic metrics for phylogenetic trees, after Sokal and Rohlf [PDF]
, 2013 Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics.
Cardona, Gabriel +4 more
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Matchings and phylogenetic trees [PDF]
Proceedings of the National Academy of Sciences, 1998 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
Diaconis, Persi W., Holmes, Susan P.
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Unrealistic phylogenetic trees may improve phylogenetic footprinting [PDF]
Bioinformatics, 2017 Abstract Motivation The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole.
Nettling, Martin +3 more
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PLoS ONE, 2015 Investigating patterns of phylogenetic structure across different life stages of tree species in forests is crucial to understanding forest community assembly, and investigating forest gap influence on the phylogenetic structure of forest regeneration is
Yi Jin, Hong Qian, Mingjian Yu
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PhySortR: a fast, flexible tool for sorting phylogenetic trees in R [PDF]
PeerJ, 2016 A frequent bottleneck in interpreting phylogenomic output is the need to screen often thousands of trees for features of interest, particularly robust clades of specific taxa, as evidence of monophyletic relationship and/or reticulated evolution. Here we
Timothy G. Stephens +3 more
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Tree-Based Unrooted Phylogenetic Networks [PDF]
Bulletin of Mathematical Biology, 2017 Abstract Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph
Francis, Andrew +2 more
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Nonbinary Tree-Based Phylogenetic Networks [PDF]
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018 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.
Laura Jetten, Leo van Iersel
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Genome rearrangements and phylogeny reconstruction in Yersinia pestis [PDF]
PeerJ, 2018 Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y.
Olga O. Bochkareva +7 more
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