Phylogenetic invariants for stationary base composition

DOI10.1016/J.JSC.2005.04.004MaRDI QIDQ2457321zbMATH OpenOpenAlexFDO

Authors Elizabeth S. Allman, John A. Rhodes

Publication date 23 October 2007

Published in Journal of Symbolic Computation (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/q-bio/0407035

zbMATH Keywords

algebraic statisticsevolution

Mathematics Subject Classification ID

Problems related to evolution (92D15) Computational aspects and applications of commutative rings (13P99) Varieties (08B99)

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.

Recommendations

• Invariants of some probability models used in phylogenetic inference
• Incorporating compositional heterogeneity into Lie Markov models for phylogenetic inference
• Phylogenetic invariants for the general Markov model of sequence mutation
• Algebraic tools for evolutionary biology
• Relevant phylogenetic invariants of evolutionary models

Cites work

• scientific article; zbMATH DE number 52497 (Why is no real title available?)
• scientific article; zbMATH DE number 3491123 (Why is no real title available?)
• scientific article; zbMATH DE number 575960 (Why is no real title available?)
• Entanglement invariants and phylogenetic branching
• Invariants of phylogenies in a simple case with discrete states
• Invariants of some probability models used in phylogenetic inference
• Phylogenetic ideals and varieties for the general Markov model
• Phylogenetic invariants for the general Markov model of sequence mutation
• Spectral analysis of phylogenetic data
• Toric Ideals of Phylogenetic Invariants
• Tropical geometry of statistical models

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

Describes a project that uses

Uses Software

• Macaulay2

This page was built for publication: Phylogenetic invariants for stationary base composition

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2457321)