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We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4...

Just over one hundred and thirty years ago Charles Darwin, in The Descent of Man and Selection in Relation to Sex (1871), developed remarkably accurate conclusions about man's ancestry, based on a review of general compa...

We need scarcely add that the contemplation in natural science of a wider domain than the actual leads to a far better understanding of the actual.' (p. 267,The, Nature of the Physical World.)x PREFACE evolutionary theor...

The MATLAB toolbox YALMIP is introduced. It is described how YALMIP can be used to model and solve optimization problems typically occurring in systems and control theory. In this paper, free MATLAB toolbox YALMIP, devel...

We consider the design of channel codes for improving the data rate and/or the reliability of communications over fading channels using multiple transmit antennas. Data is encoded by a channel code and the encoded data i...

Conventional approaches to sampling signals or images follow Shannon's theorem: the sampling rate must be at least twice the maximum frequency present in the signal (Nyquist rate). In the field of data conversion, standa...

We propose a novel image denoising strategy based on an enhanced sparse representation in transform domain. The enhancement of the sparsity is achieved by grouping similar 2-D image fragments (e.g., blocks) into 3-D data...

Even if there is an agreed-upon, fixed social objective function and policymakers know the timing and magnitude of the effects of their actions, discretionary policy, namely, the selection of that decision which is best,...

This note considers the problem of information consensus among multiple agents in the presence of limited and unreliable information exchange with dynamically changing interaction topologies. Both discrete and continuous...

Many problems of recent interest in statistics and machine learning can be posed in the framework of convex optimization. Due to the explosion in size and complexity of modern datasets, it is increasingly important to be...

Preface to the Second Edition. Preface to the First Edition. Acknowledgments for the Second Edition. Acknowledgments for the First Edition. 1. Introduction and Preview. 1.1 Preview of the Book. 2. Entropy, Relative Entro...

Due to the simplicity of their implementations, least square support vector machine (LS-SVM) and proximal support vector machine (PSVM) have been widely used in binary classification applications. The conventional LS-SVM...

FOUNDATIONS. The Scope of Integer and Combinatorial Optimization. Linear Programming. Graphs and Networks. Polyhedral Theory. Computational Complexity. Polynomial-Time Algorithms for Linear Programming. Integer Lattices....

1. Fundamental Concepts. Definitions and examples. Paths and proofs. Vertex degrees and counting. Degrees and algorithmic proof. 2. Trees and Distance. Basic properties. Spanning trees and enumeration. Optimization and t...

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. He...

The Gibbs sampler, the algorithm of Metropolis and similar iterative simulation methods are potentially very helpful for summarizing multivariate distributions. Used naively, however, iterative simulation can give mislea...

We introduce a stable, well tested Python implementation of the affine-invariant ensemble sampler for Markov chain Monte Carlo (MCMC) proposed by Goodman & Weare (2010). The code is open source and has already been used ...

This paper describes a graph-theoretic complexity measure and illustrates how it can be used to manage and control program complexity. The paper first explains how the graph-theory concepts apply and gives an intuitive e...

Although the problem of determining the minimum cost path through a graph arises naturally in a number of interesting applications, there has been no underlying theory to guide the development of efficient search procedu...

An approach to the general problem of signal parameter estimation is described. The algorithm differs from its predecessor in that a total least-squares rather than a standard least-squares criterion is used. Although di...

BACKGROUND: We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacr...

"An IEEE reprinting of this classic 1968 edition, FIELD COMPUTATION BY MOMENT METHODS is the first book to explore the computation of electromagnetic fields by the most popular method for the numerical solution to electr...

Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into ...

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= nei...