title: constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints.
abstract: This article introduces constNJ (constrained neighbor-joining), an algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune-regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees that must fit into a recombination, hybridization, or similar network. Rather than first finding a set of trees that are optimal according to a phylogenetic criterion (e.g., likelihood or parsimony) and then attempting to fit them into a network, constNJ estimates the trees while enforcing specified rSPR distance constraints. The primary input for constNJ is a collection of distance matrices derived from sequence blocks which are assumed to have evolved in a tree-like manner, such as blocks of an alignment which do not contain any recombination breakpoints. The other input is a set of rSPR constraint inequalities for any set of pairs of trees. constNJ is consistent and a strict generalization of the neighbor-joining algorithm; it uses the new notion of maximum agreement partitions (MAPs) to assure that the resulting trees satisfy the given rSPR distance constraints.
authors.affiliation: Program in Computational Biology, Fred Hutchinson Cancer Research Center 1100, Seattle, Washington 98109-1024, USA. matsen@fhcrc.org
authors.forename: Frederick A
authors.initials: FA
authors.lastname: Matsen
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030541:Databases, Genetic; D006678:HIV / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment