The space of ultrametric phylogenetic trees

DOI10.1016/j.jtbi.2016.05.001zbMath1343.92343arXiv1410.3544OpenAlexW1786054391WikidataQ39759719 ScholiaQ39759719MaRDI QIDQ307584

Alex Gavryushkin, Alexei J. Drummond

Publication date: 5 September 2016

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1410.3544

zbMATH Keywords

curvaturesimplicial complexgeodesicphylogenetic treeCAT(0)phylogenetic inferenceposterior distribution summarytime-treeultrametric tree

Mathematics Subject Classification ID

Problems related to evolution (92D15) Applications of graph theory (05C90)

Related Items

Zig-Zag Sampling for Discrete Structures and Nonreversible Phylogenetic MCMC ⋮ Phylogenetic network dissimilarity measures that take branch lengths into account ⋮ Old and new challenges in Hadamard spaces ⋮ Introducing a general class of species diversification models for phylogenetic trees ⋮ Convexity in Tree Spaces ⋮ The space of equidistant phylogenetic cactuses ⋮ Random walks and Brownian motion on cubical complexes ⋮ New Gromov-inspired metrics on phylogenetic tree space ⋮ Computing nearest neighbour interchange distances between ranked phylogenetic trees ⋮ The combinatorics of discrete time-trees: theory and open problems ⋮ Discrete coalescent trees ⋮ The geometry of partial fitness orders and an efficient method for detecting genetic interactions ⋮ Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models ⋮ Kantorovich-Rubinstein distance and barycenter for finitely supported measures: foundations and algorithms ⋮ Finite metric and 𝑘-metric bases on ultrametric spaces

Uses Software

• BEAST
• PhyloNetwork

Cites Work

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• Central limit theorems for Fréchet means in the space of phylogenetic trees
• Sticky central limit theorems on open books
• Nodal distances for rooted phylogenetic trees
• Principal components analysis in the space of phylogenetic trees
• Simplicial nonpositive curvature
• Geometry of the space of phylogenetic trees
• Polyhedral computational geometry for averaging metric phylogenetic trees
• The Bergman complex of a matroid and phylogenetic trees
• Computing Geodesic Distances in Tree Space
• Riemannian center of mass and mollifier smoothing
• On the Generalized "Birth-and-Death" Process