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Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Frederick A Matsen* and Aaron Gallagher

Author Affiliations

Fred Hutchinson Cancer Research Center, Seattle, Washington, USA

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Algorithms for Molecular Biology 2012, 7:8  doi:10.1186/1748-7188-7-8

Published: 2 May 2012



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.


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.


The algorithms in this paper, and the associated freely-available software, will help biologists better use and understand taxonomically labeled phylogenetic trees.

phylogenetics; taxononomy; dynamic program; branch and bound; convex coloring; algorithms