Phylogenetic invariants for stationary base composition
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Publication:2457321
DOI10.1016/J.JSC.2005.04.004zbMATH Open1120.92031arXivq-bio/0407035OpenAlexW1977411708MaRDI QIDQ2457321FDOQ2457321
Authors: Elizabeth S. Allman, John A. Rhodes 
Publication date: 23 October 2007
Published in: Journal of Symbolic Computation (Search for Journal in Brave)
Abstract: Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent evolution may lead to similar base frequencies emerging from different lineages. To study this situation, algebraic models of biological sequence evolution are introduced in which the base composition is fixed throughout evolution. Basic properties of the associated algebraic varieties are investigated, including the construction of some phylogenetic invariants.
Full work available at URL: https://arxiv.org/abs/q-bio/0407035
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Problems related to evolution (92D15) Computational aspects and applications of commutative rings (13P99) Varieties (08B99)
Cites Work
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- Tropical geometry of statistical models
- Invariants of phylogenies in a simple case with discrete states
- Phylogenetic invariants for the general Markov model of sequence mutation
- Invariants of some probability models used in phylogenetic inference
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Cited In (8)
- Cayley's hyperdeterminant: A combinatorial approach via representation theory
- A novel algebraic approach to time-reversible evolutionary models
- Advanced formulation of base pair changes in the stem regions of ribosomal RNAs; its application to mitochondrial rRNAs for resolving the phylogeny of animals
- The hyperdeterminant and triangulations of the 4-cube
- Phylogenetic ideals and varieties for the general Markov model
- Topics on phylogenetic algebraic geometry
- Conditional independence ideals with hidden variables
- Low degree equations for phylogenetic group-based models
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