Phylogenetic diversity and the maximum coverage problem

Moulton, Vincent; Spillner, Andreas

doi:10.1016/j.aml.2009.03.017

Cited by 3 publications

(3 citation statements)

References 27 publications

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“…This approach aims to avoid choosing cells that are only distinguished by their relative ease of amplification, but may otherwise not be particularly rich in novel information. When originally searching for a solution to this problem we were inspired by the proposed solutions to the species prioritization problem in conservation biology [ 49 , 50 ], specifically choosing a mixed integer programming approach. The criterion used to assess amplification dynamics was computed as the time needed to reach the inflection point in the amplification curve, which was supplied as the per-cell “cost” to the optimization procedure.…”

Section: Methodsmentioning

confidence: 99%

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community

Lyalina

Stepanauskas

et al. 2022

PLoS ONE

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Laboratory mice are widely studied as models of mammalian biology, including the microbiota. However, much of the taxonomic and functional diversity of the mouse gut microbiome is missed in current metagenomic studies, because genome databases have not achieved a balanced representation of the diverse members of this ecosystem. Towards solving this problem, we used flow cytometry and low-coverage sequencing to capture the genomes of 764 single cells from the stool of three laboratory mice. From these, we generated 298 high-coverage microbial genome assemblies, which we annotated for open reading frames and phylogenetic placement. These genomes increase the gene catalog and phylogenetic breadth of the mouse microbiota, adding 135 novel species with the greatest increase in diversity to the Muribaculaceae and Bacteroidaceae families. This new diversity also improves the read mapping rate, taxonomic classifier performance, and gene detection rate of mouse stool metagenomes. The novel microbial functions revealed through our single-cell genomes highlight previously invisible pathways that may be important for life in the murine gastrointestinal tract.

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Section: Methodsmentioning

confidence: 99%

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community

Lyalina

Stepanauskas

et al. 2022

PLoS ONE

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“…We wish to point out that the theory of matroids has touched phylogenetics also in many other contexts, see e.g. [2,3,17,22,27,48,49,51,59].…”

Section: Introductionmentioning

confidence: 99%

The matroid structure of representative triple sets and triple-closure computation

Seemann

Hellmuth

2018

European Journal of Combinatorics

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“…We wish to point out that the theory of matroids has touched phylogenetics also in many other contexts, see e.g. [2,3,17,22,27,48,49,51,59].…”

Section: Introductionmentioning

confidence: 99%

The Matroid Structure of Representative Triple Sets and Triple-Closure Computation

Hellmuth,

Seemann

2017

Preprint

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The closure cl(R) of a consistent set R of triples (rooted binary trees on three leaves) provides essential information about tree-like relations that are shown by any supertree that displays all triples in R. In this contribution, we are concerned with representative triple sets, that is, subsets R of R with cl(R ) = cl(R). In this case, R still contains all information on the tree structure implied by R, although R might be significantly smaller. We show that representative triple sets that are minimal w.r.t. inclusion form the basis of a matroid. This in turn implies that minimal representative triple sets also have minimum cardinality. In particular, the matroid structure can be used to show that minimum representative triple sets can be computed in polynomial time with a simple greedy approach. For a given triple set R that "identifies" a tree, we provide an exact value for the cardinality of its minimum representative triple sets. In addition, we utilize the latter results to provide a novel and efficient method to compute the closure cl(R) of a consistent triple set R that improves the time complexity O(|R||L R | 4 ) of the currently fastest known method proposed by Bryant and Steel (1995). In particular, if a minimum representative triple set for R is given, it can be shown that the time complexity to compute cl(R) can be improved by a factor up to |R||L R |. As it turns out, collections of quartets (unrooted binary trees on four leaves) do not provide a matroid structure, in general.

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Phylogenetic diversity and the maximum coverage problem

Cited by 3 publications

References 27 publications

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community

The matroid structure of representative triple sets and triple-closure computation

The Matroid Structure of Representative Triple Sets and Triple-Closure Computation

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