The combinatorics of discrete time-trees: theory and open problems

DOI10.1007/s00285-017-1167-9zbMath1391.92030OpenAlexW2951449384WikidataQ47746550 ScholiaQ47746550MaRDI QIDQ96717

Frederick A. IV Matsen, Alex Gavryushkin, Chris Whidden, Chris Whidden, Frederick A. IV Matsen

Publication date: 29 July 2017

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

Full work available at URL: https://doi.org/10.1007/s00285-017-1167-9

zbMATH Keywords

nearest neighbor interchange graphphylogenetic inference methodsphylogenetic time-tree

Mathematics Subject Classification ID

Trees (05C05) Problems related to evolution (92D15) Combinatorics in computer science (68R05) Graph theory (including graph drawing) in computer science (68R10) Genetics and epigenetics (92D10)

Related Items (6)

Ranked subtree prune and regraft ⋮ Computing nearest neighbour interchange distances between ranked phylogenetic trees ⋮ Discrete coalescent trees ⋮ rrnni ⋮ 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

Uses Software

• LAMARC

Cites Work

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• The space of ultrametric phylogenetic trees
• Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies
• Limitations of Markov chain Monte Carlo algorithms for Bayesian inference of phylogeny
• Geometry of the space of phylogenetic trees
• Ricci-Ollivier curvature of the rooted phylogenetic subtree-prune-regraft graph
• A note on the relaxation time of two Markov chains on rooted phylogenetic tree spaces
• Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach
• Fast Convergence of Markov Chain Monte Carlo Algorithms for Phylogenetic Reconstruction with Homogeneous Data on Closely Related Species
• Short Encodings of Evolving Structures
• Some notes on the nearest neighbour interchange distance

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