Representations of partial leaf sets in phylogenetic tree space

DOI10.1137/18M1235855MaRDI QIDQ5208889zbMATH OpenOpenAlexWikidataFDO

Authors Gillian Roxanne Grindstaff, Megan Owen

Publication date 22 January 2020

Published in SIAM Journal on Applied Algebra and Geometry (Search for Journal in Brave)

Full work available at URL https://epubs.siam.org/doi/pdf/10.1137/18M1235855

zbMATH Keywords

dimensionality reductionphylogenetic reconstructionphylogenetic treessupertreetree space

Mathematics Subject Classification ID

Trees (05C05) Combinatorial complexity of geometric structures (52C45) Problems related to evolution (92D15)

Recommendations

• Extension operations on sets of leaf-labelled trees
• A supertree method for rooted trees
• Geometry of the space of phylogenetic trees
• Consensus supertrees: The synthesis of rooted trees containing overlapping sets of labeled leaves
• Constructing rooted supertrees using distances

Cites work

• A New Algorithm for Generating All the Maximal Independent Sets
• Computing geodesic distances in tree space
• Computing medians and means in Hadamard spaces
• Confidence Sets for Phylogenetic Trees
• Geometry of the space of phylogenetic trees
• Phylogenetic supertrees. Combining information to reveal the tree of life
• Polyhedral computational geometry for averaging metric phylogenetic trees

Cited in

(9)

• Geometry of the space of phylogenetic trees
• On the approximability of the fixed-tree balanced minimum evolution problem
• Wald space for phylogenetic trees
• A partial order and cluster-similarity metric on rooted phylogenetic trees
• A navigation system for tree space
• The ultrametric Gromov-Wasserstein distance
• Stratifying the space of barcodes using Coxeter complexes
• Probability metrics for tropical spaces of different dimensions
• Geometry of the space of phylogenetic trees with non-identical leaves

Describes a project that uses

Uses Software

• BEAST
• Phylo-MCOA
• kdetrees
• ASTRAL-II
• PhyloNet

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