Tree Construction using Singular Value Decomposition

DOI10.1017/CBO9780511610684.023MaRDI QIDQ4594317zbMATH OpenOpenAlexFDO

Authors Nicholas Eriksson

Publication date 23 November 2017

Published in Algebraic Statistics for Computational Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1017/cbo9780511610684.023

Mathematics Subject Classification ID

Permutations, words, matrices (05A05) Markov chains (discrete-time Markov processes on discrete state spaces) (60J10) Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Problems related to evolution (92D15)

Cited in

(12)

• Dimensional reduction for the general Markov model on phylogenetic trees
• Local equations for equivariant evolutionary models
• Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites
• Parsimony and the rank of a flattening matrix
• Identifiability of large phylogenetic mixture models
• Spectral neighbor joining for reconstruction of latent tree models
• H-representation of the Kimura-3 polytope for the m-claw tree
• Rank conditions on phylogenetic networks
• Phylogenetic reconstruction based on algebra
• Computing implicitizations of multi-graded polynomial maps
• Relevant phylogenetic invariants of evolutionary models
• Geometry of the Kimura 3-parameter model

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