Optimality of the neighbor joining algorithm and faces of the balanced minimum evolution polytope
From MaRDI portal
(Redirected from Publication:263784)
Abstract: Balanced minimum evolution (BME) is a statistically consistent distance-based method to reconstruct a phylogenetic tree from an alignment of molecular data. In 2000, Pauplin showed that the BME method is equivalent to optimizing a linear functional over the BME polytope, the convex hull of the BME vectors obtained from Pauplin's formula applied to all binary trees. The BME method is related to the Neighbor Joining (NJ) algorithm, now known to be a greedy optimization of the BME principle. Further, the NJ and BME algorithms have been studied previously to understand when the NJ Algorithm returns a BME tree for small numbers of taxa. In this paper we aim to elucidate the structure of the BME polytope and strengthen knowledge of the connection between the BME method and NJ Algorithm. We first prove that any subtree-prune-regraft move from a binary tree to another binary tree corresponds to an edge of the BME polytope. Moreover, we describe an entire family of faces parametrized by disjoint clades. We show that these {em clade-faces} are smaller dimensional BME polytopes themselves. Finally, we show that for any order of joining nodes to form a tree, there exists an associated distance matrix (i.e., dissimilarity map) for which the NJ Algorithm returns the BME tree. More strongly, we show that the BME cone and every NJ cone associated to a tree have an intersection of positive measure.
Recommendations
Cites work
- A canonical decomposition theory for metrics on a finite set
- Computational complexity of inferring phylogenies from dissimilarity matrices
- Cyclic permutations and evolutionary trees
- Efficiently Calculating Evolutionary Tree Measures Using SAT
- scientific article; zbMATH DE number 4089320 (Why is no real title available?)
- scientific article; zbMATH DE number 1945176 (Why is no real title available?)
- On the consistency of the minimum evolution principle of phylogenetic inference
- On the uniqueness of the selection criterion in neighbor-joining
- Polyhedral geometry of phylogenetic rogue taxa
- The Geometry of the Neighbor-Joining Algorithm for Small Trees
Cited in
(19)- Fast neighbor joining
- Polyhedral combinatorics of UPGMA cones
- Enumerating vertices of the balanced minimum evolution polytope
- On the approximability of the fixed-tree balanced minimum evolution problem
- An information theory perspective on the balanced minimum evolution problem
- Level-1 phylogenetic networks and their balanced minimum evolution polytopes
- Split network polytopes and network spaces
- Split-facets for balanced minimal evolution polytopes and the permutoassociahedron
- A tutorial on the balanced minimum evolution problem
- Facets of the balanced minimal evolution polytope
- Robustness of Greedy Type Minimum Evolution Algorithms
- The Geometry of the Neighbor-Joining Algorithm for Small Trees
- Polyhedral geometry of phylogenetic rogue taxa
- A massively parallel branch-\&-bound algorithm for the balanced minimum evolution problem
- Robustness of phylogenetic inference based on minimum evolution
- Optimizing over path-length matrices of unrooted binary trees
- A note on the approximability of the balanced minimum evolution problem
- On the balanced minimum evolution polytope
- On the uniqueness of the selection criterion in neighbor-joining
This page was built for publication: Optimality of the neighbor joining algorithm and faces of the balanced minimum evolution polytope
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q263784)
