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 accordin...

PURPOSE The purpose of this study was to assess the relationship between donor factors and 5-year corneal graft survival in the Cornea Donor Study. METHODS Donor corneas met criteria established by the Eye Bank Association of America, had an endothelial cell density of 2300 to 3300/mm, and were determined to be of good to excellent quality by the eye banks. Donor corneas were assigned using a...

In order to gain an understanding of the effectiveness of phylogenetic Markov chain Monte Carlo (MCMC), it is important to understand how quickly the empirical distribution of the MCMC converges to the posterior distribution. In this article, we investigate this problem on phylogenetic tree topologies with a metric that is especially well suited to the task: the subtree prune-and-regraft (SPR) ...

PURPOSE To evaluate the data of penetrating keratoplasty over a 10-year period and to compare indications and outcomes of eyes undergoing single graft with those of eyes requiring regrafting. METHODS A total of 652 eyes of 613 patients required single graft (Group I). Sixty-one regrafts were performed on 53 eyes (Group II). The mean follow-up time was 23.4+/-21.3 months (range 6-132 months). ...

The SPR (subtree prune and regraft) operation is used as the basis for reconciling incongruent phylo-genetic trees, particularly for detecting and analyzing non-treelike evolutionary histories such as horizontal gene transfer, hybrid speciation, and recombination. The SPR-based tree reconciliation problem has been shown to be NP-hard, and several efficient heuristics have been designed to solve...

We study subtree-prune-and-regraft (SPR) operations on leaf-labelled rooted binary trees, also known as rooted binary phylogenetic trees. This study is motivated by the problem of graphically representing evolutionary histories of biological sequences subject to recombination. We investigate some basic properties of the induced SPR-metric on the space r n of leaf-labelled rooted binary trees wi...

We develop techniques to calculate important measures in evolutionary biology by encoding to CNF formulas and using powerful SAT solvers. Comparing evolutionary trees is a necessary step in tree reconstruction algorithms, locating recombination and lateral gene transfer, and in analyzing and visualizing sets of trees. We focus on two popular comparison measures for trees: the hybridization numb...

The subtree prune and regraft distance (d(SPR)) between phylogenetic trees is important both as a general means of comparing phylogenetic tree topologies as well as a measure of lateral gene transfer (LGT). Although there has been extensive study on the computation of d(SPR) and similar metrics between rooted trees, much less is known about SPR distances for unrooted trees, which often arise in...

BACKGROUND To investigate the outcome and prognostic factors for corneal graft recovery after severe corneal graft rejection following penetrating keratoplasty (PKP) treated with topical and systemic steroids. METHODS Fifty-eight eyes in 58 patients with severe corneal graft rejection following PKP were treated with topical and systemic steroids. Factors affecting the reversibility and mainte...

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 ...