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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)

- David Sankoff, Yvon Abel, J. Hein
- 2005

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)

- Jochen Hein
- 2008

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)

- G A Lunter, I Miklós, Y S Song, J Hein
- 2003

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)

- Jochen Hein
- 1999

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