Who is Who in Phylogenetic Networks

Publications related to 'Program constNJ' : constNJ is an OCaml program which takes as input a set of distances matrices and implicitly reconstructs a phylogenetic network: it infers, for each of those matrices, a corresponding phylogenetic tree, with some constraints on the upper bound of the SPR-distance between those reconstructed trees. Available at http://www.stat.berkeley.edu/~matsen/constNJ/.   Order by:   Type | Year

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from-distances Program-constNJ reconstruction

2010

1 Frederick A. Matsen. ConstNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints. In JCB, Vol. 17(6):799-818, 2010. Keywords: from distances, Program constNJ, reconstruction. Note: http://arxiv.org/abs/0901.1598v2.         Toggle 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. Copyright 2010, Mary Ann Liebert, Inc."