Among the fundamental problems in molecular evolution and in the analysis of homologous sequences are alignment, phylogeny reconstruction, and the reconstruction of ancestral sequences. This paper presents a fast, combined solution to these problems. The new algorithm gives an approximation to the minimal history in terms of a distance function on… (More)
A fast method for reconstructing phylogenies from distance data is presented. The method is economical in the number of pairwise comparisons needed. It can be combined with a new phylogenetic alignment procedure to yield an algorithm that gives a complete history of a set of homologous sequences. The method is applicable to very large distance matrices. An… (More)
The method of nearest-neighbor interchange effects local improvements in a binary tree by replacing a 4-subtree by one of its two alternatives if this improves the objective function. We extend this to k-subtrees to reduce the number of local optima. Possible sequences of k-subtrees to be examined are produced by moving a window over the tree, incorporating… (More)
We describe the bottomonium spectrum obtained on the UKQCD dynamical ensembles and its comparison to quenched results. We include a determination of αs and m b from the dynamical results.
We describe the first lattice determination of the strong coupling constant with 3 flavors of dynamical quarks. The method follows previous analyses in using a perturbative expansion for the plaquette and Upsilon spectroscopy to set the scale. Using dynamical configurations from the MILC collaboration with 2+1 flavors of dynamical quarks we are able to… (More)
In our nonperturbative lattice investigation we study the interface tension of the finite-temperature electroweak phase transition. In this analysis the Higgs mass has been chosen to be about 35 GeV. At the transition point of a finite volume system, tunnelling between the symmetric and the Higgs phase takes place. This phenomenon leads to a splitting of… (More)
Documentation License, Version 1.1 or any later version published by the Free Software Foundation; with no Invariant Sections , with the no Front-Cover Texts, and with no Back-Cover Texts. A copy of the license is included in the section entitled "GNU Free Documentation License". This is still a DRAFT only. I need to decide how to use the options available… (More)
We present an ef cient algorithm for statistical multiple alignment based on the TKF91 model of Thorne, Kishino, and Felsenstein (1991) on an arbitrary k-leaved phylogenetic tree. The existing algorithms use a hidden Markov model approach, which requires at least O. p 5 k / states and leads to a time complexity of O.5 k L k /, where L is the geometric mean… (More)