Numerical Algebraic Geometry for Analysis of Phylogenetic Trees
نویسندگان
چکیده
Using tools from numerical algebraic geometry, we propose a phylogenetic reconstruction algorithm which uses the distance to the nearest point on the phylogenetic model to select the tree of best fit. This method allows for the reconstruction of branch lengths and for hypothesis testing. A data-dependent statistical test identifies correctly reconstructed quartet trees 100% of the time when the p-value associated to the nearest phylogenetic model is greater than .99. Keywords—phylogenetic invariants, numerical algebraic geometry, quartets.
منابع مشابه
Phylogenetic Algebraic Geometry
Phylogenetic algebraic geometry is concerned with certain complex projective algebraic varieties derived from finite trees. Real positive points on these varieties represent probabilistic models of evolution. For small trees, we recover classical geometric objects, such as toric and determinantal varieties and their secant varieties, but larger trees lead to new and largely unexplored territory...
متن کاملSyntactic Phylogenetic Trees
In light of recent controversies surrounding the use of computational methods for the reconstruction of phylogenetic trees of language families (especially the Indo-European family), a possible approach based on syntactic information, complementing other linguistic methods, appeared as a promising possibility, largely developed in recent years in Longobardi’s Parametric Comparison Method. In th...
متن کاملGeometry of time-reversible group-based models
Phylogenetic models have polynomial parametrization maps. For symmetric group-based models, Matsen studied the polynomial inequalities that characterize the joint probabilities in the image of these parametrizations [19]. We employ this description for maximum likelihood estimation via numerical algebraic geometry. In particular, we explore an example where the maximum likelihood estimate does ...
متن کاملQuantitative Comparison of Tree Pairs Resulted from Gene and Protein Phylogenetic Trees for Sulfite Reductase Flavoprotein Alpha-Component and 5S rRNA and Taxonomic Trees in Selected Bacterial Species
Introduction: FAD is the cofactor of FAD-FR protein family. Sulfite reductase flavoprotein alpha-component is one of the main enzymes of this family. Based on applications of this enzyme in biotechnology and industry, it was chosen as the subject of evolutionary studies in 19 specific species. Method: Gene and protein sequences of sulfite reductase flavoprotein alpha-component, 5S rRNA sequence...
متن کاملAlgebraic distances for phylogenetic trees
We propose several new distances for phylogenetic trees based on two new algebraic representations of them as permutations and as monomial ideals.
متن کامل