Maximum likelihood estimation for unrooted 3-leaf trees: an analytic solution for the CFN model

DOI10.1007/S11538-024-01340-XzbMATH Open1546.92086MaRDI QIDQ6601313FDOQ6601313

Authors: Max Hill, Sebastien Roch, Jose Israel Rodriguez 

Publication date: 10 September 2024

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

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zbMATH Keywords

maximum likelihoodphylogeneticsphylogenetic treesCFN modelsemi-algebraic constraintsgroup based models

Mathematics Subject Classification ID

Problems related to evolution (92D15) Protein sequences, DNA sequences (92D20)

Cites Work

• Elements of Information Theory
• Title not available (Why is that?)
• A combinatorial description of the closest tree algorithm for finding evolutionary trees
• Invariants of some probability models used in phylogenetic inference
• A discrete Fourier analysis for evolutionary trees.
• Toric Ideals of Phylogenetic Invariants
• The maximum likelihood degree of mixtures of independence models
• Solving the likelihood equations
• Analytic solutions for three taxon ML trees with variable rates across sites
• Toric geometry of the Cavender-Farris-Neyman model with a molecular clock
• Spectral analysis of phylogenetic data
• Algebraic statistics
• Maximum likelihood estimation of the latent class model through model boundary decomposition
• Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry
• Distance to the stochastic part of phylogenetic varieties
• The model-specific Markov embedding problem for symmetric group-based models
• Logarithmic cotangent bundles, Chern‐Mather classes, and the Huh‐Sturmfels involution conjecture
• Maximum likelihood estimation and natural pairwise estimating equations are identical for three sequences and a symmetric 2-state substitution model

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