Results 51 to 60 of about 2,017,394 (267)
Identifying phylogenetic trees
Discrete Mathematics, 2005 AbstractA central problem that arises in evolutionary biology is that of displaying partitions of subsets of a finite set X on a tree whose vertices are partially labelled with the elements of X. Such a tree is called an X-tree and, for a collection C of partitions of subsets of X, characterisations for the existence and uniqueness of an X-tree that ...
Bordewich, Magnus +2 more
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A Stochastic Model for Phylogenetic Trees [PDF]
Journal of Applied Probability, 2009 We propose the following simple stochastic model for phylogenetic trees. New types are born and die according to a birth and death chain. At each birth we associate a fitness to the new type sampled from a fixed distribution. At each death the type with the smallest fitness is killed. We show that if the birth (i.e.
Rinaldo B. Schinazi, Thomas M. Liggett
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ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates
Nature Methods, 2017 Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic ...
S. Kalyaanamoorthy +4 more
semanticscholar +1 more source
Cancer phylogenetic tree inference at scale from 1000s of single cell genomes
bioRxiv, 2020 A new generation of scalable single cell whole genome sequencing (scWGS) methods allows unprecedented high resolution measurement of the evolutionary dynamics of cancer cell populations.
Sohrab Salehi +14 more
semanticscholar +1 more source
Mitochondrial DNA. Part B. Resources, 2021 We determined a complete mitochondrial genome of Episoriculus leucops. This mitogenome is a circular molecule with 16,838 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes (tRNA), and two ribosomal RNA genes (rRNA).
Dan Chen +4 more
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Phylogenetic mixtures on a single tree can mimic a tree of another topology [PDF]
, 2007 Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent debate.
Matsen, Frederick A., Steel, Mike
core +3 more sources
Novel metric for hyperbolic phylogenetic tree embeddings
bioRxiv, 2020 Advances in experimental technologies such as DNA sequencing have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of ...
Hirotaka Matsumoto +2 more
semanticscholar +1 more source
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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A matroid associated with a phylogenetic tree [PDF]
Discrete Mathematics & Theoretical Computer Science, 2014 Special issue PRIMA 2013 A (pseudo-)metric D on a finite set X is said to be a \textquotelefttree metric\textquoteright if there is a finite tree with leaf set X and non-negative edge weights so that, for all x,y ∈X, D(x,y) is the path distance in the tree between x and y. It is well known that not every metric is a tree metric. However, when
Dress, Andreas +2 more
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Molecular biology and evolution, 2019 Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different ...
Li-Gen Wang +13 more
semanticscholar +1 more source