reconciling taxonomy and phylogenetic inference formalism and algorithms for describing discord and inferring taxonomic roots调和分类和系统发育推断形式和算法描述不和和推断的根源.pdfVIP

Matsen and Gallagher Algorithms for Molecular Biology 2012, 7:8 /content/7/1/8 RESEARCH Open Access Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots * Frederick A Matsen and Aaron Gallagher Abstract Background: Although taxonomy is often used informally to evaluate the results of phylogenetic inference and the root of phylogenetic trees, algorithmic methods to do so are lacking. Results: In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a “subcoloring” problem to express the difference between a taxonomy and a phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. Conclusions: The algorithms in this paper, and the associated freely-available software, will help biologists better use and understand taxonomically labeled phylogenetic trees. Keywords: phylogenetics, taxononomy, dynamic program, branch and bound, convex coloring, algorithms Background for classifications. These tools aim to update taxonomies Since the beginnings of phylogenetics, researchers have to be closer to phylogenetic inferences. used a combination of phylogenetic inference and taxo- In this paper we approach the commonly encountered nomic knowledge to understand evolutionary relation- simpler problem of a researcher inf