Phylogenetic invariants for the general Markov model of sequence mutation
From MaRDI portal
Publication:1417839
DOI10.1016/j.mbs.2003.08.004zbMath1031.92019OpenAlexW2060967837WikidataQ79218669 ScholiaQ79218669MaRDI QIDQ1417839
John A. Rhodes, Elizabeth S. Allman
Publication date: 6 January 2004
Published in: Mathematical Biosciences (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1016/j.mbs.2003.08.004
Problems related to evolution (92D15) Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20)
Related Items
Local equations for equivariant evolutionary models ⋮ Markov invariants and the isotropy subgroup of a quartet tree ⋮ Topics on phylogenetic algebraic geometry ⋮ Transforming phylogenetic networks: moving beyond tree space ⋮ Approximation by matrices with simple spectra ⋮ Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants ⋮ Geometry and the complexity of matrix multiplication ⋮ Decomposition Algorithms for Tensors and Polynomials ⋮ Generating Markov evolutionary matrices for a given branch length ⋮ Phylogenomic Models from Tree Symmetries ⋮ Identifiability of large phylogenetic mixture models ⋮ Parsimony and the rank of a flattening matrix ⋮ An algebraic analysis of the two state Markov model on tripod trees ⋮ Estimating trees from filtered data: identifiability of models for morphological phylogenetics ⋮ Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent ⋮ Phylogenetic invariants for stationary base composition ⋮ Distance to the stochastic part of phylogenetic varieties ⋮ The model-specific Markov embedding problem for symmetric group-based models ⋮ Preface. Algebraic methods in phylogenetics ⋮ Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry ⋮ Geometry of the Kimura 3-parameter model ⋮ Phylogenetic ideals and varieties for the general Markov model ⋮ Toward a Salmon Conjecture ⋮ Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites ⋮ Ideals of varieties parameterized by certain symmetric tensors ⋮ The Spacey Random Walk: A Stochastic Process for Higher-Order Data ⋮ A proof of the set-theoretic version of the salmon conjecture ⋮ Relevant phylogenetic invariants of evolutionary models ⋮ Partially Symmetric Variants of Comon's Problem Via Simultaneous Rank ⋮ Markov invariants, plethysms, and phylogenetics ⋮ The Rise of Statistical Phylogenetics ⋮ Tropical geometry of statistical models ⋮ Semialgebraic Geometry of Nonnegative Tensor Rank ⋮ On approximately simultaneously diagonalizable matrices ⋮ Low degree equations for phylogenetic group-based models ⋮ Systematics and symmetry in molecular phylogenetic modelling: perspectives from physics
Cites Work
- Invariants of phylogenies in a simple case with discrete states
- Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.
- Reconstructing phylogenies from nucleotide pattern probabilities: A survey and some new results
- Recovering a tree from the leaf colourations it generates under a Markov model
- Determining the number and structure of phylogenetic invariants.
- On the ideals of secant varieties of Segre varieties
- Spectral analysis of phylogenetic data
- A remarkable nonlinear invariant for evolution with heterogeneous rates
- Tree representations of non-symmetric group-valued proximities
- Commuting pairs and triples of matrices and related varieties
- Invariants of some probability models used in phylogenetic inference
- A note on commuting pairs of matrices
- The empirical discovery of phylogenetic invariants