We consider n points (nodes), some or all pairs of which are connected by a branch; the length of each branch is given. We restrict ourselves to the case where at least one path exists between any two nodes. We now consider two problems. Problem 1. Constrnct the tree of minimum total length between the n nodes. (A tree is a graph with one and only one path between every two nodes.) In the course of the construction that we present here, the branches are subdivided into three sets: I. the branches definitely assignec~ to the tree under construction (they will form a subtree) ; II. the branches from which the next branch to be added to set I, will be selected ; III. the remaining branches (rejected or not yet considered). The nodes are subdivided into two sets: A. the nodes connected by the branches of set I, B. the remaining nodes (one and only one branch of set II will lead to each of these nodes), We start the construction by choosing an arbitrary node as the only member of set A, and by placing all branches that end in this node in set II. To start with, set I is empty. From then onwards we perform the following two steps repeatedly. Step 1. The shortest branch of set II is removed from this set and added to

/pdf/a-note-on-two-problems-in-connexion-with-graphs-4btl91o8g9.pdf

A note on two problems in connexion with graphs

Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.

/pdf/arlequin-version-3-0-an-integrated-software-package-for-4cs6nd3y2p.pdf

Arlequin (version 3.0): An integrated software package for population genetics data analysis

Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolutionary paths in the form of cycles. We present a method ("median joining" [MJ]) for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that our MJ method does not resolve ties. The MJ method is hence closely related to the earlier approach of Foulds, Hendy, and Penny for estimating MP trees but can be adjusted to the level of homoplasy by setting a parameter epsilon. Unlike our earlier reduced median (RM) network method, MJ is applicable to multistate characters (e.g., amino acid sequences). An additional feature is the speed of the implemented algorithm: a sample of 800 worldwide mtDNA hypervariable segment I sequences requires less than 3 h on a Pentium 120 PC. The MJ method is demonstrated on a Tibetan mitochondrial DNA RFLP data set.

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Median-joining networks for inferring intraspecific phylogenies.

An essential textbook for any student or researcher in biology needing to design experiments, sample programs or analyse the resulting data The text begins with a revision of estimation and hypothesis testing methods, covering both classical and Bayesian philosophies, before advancing to the analysis of linear and generalized linear models Topics covered include linear and logistic regression, simple and complex ANOVA models (for factorial, nested, block, split-plot and repeated measures and covariance designs), and log-linear models Multivariate techniques, including classification and ordination, are then introduced Special emphasis is placed on checking assumptions, exploratory data analysis and presentation of results The main analyses are illustrated with many examples from published papers and there is an extensive reference list to both the statistical and biological literature The book is supported by a website that provides all data sets, questions for each chapter and links to software

/pdf/experimental-design-and-data-analysis-for-biologists-8ybva8d53x.pdf

Experimental Design and Data Analysis for Biologists

From the Publisher:
With this text, you gain an understanding of the fundamental concepts of algorithms, the very heart of computer science. It introduces the basic data structures and programming techniques often used in efficient algorithms. Covers use of lists, push-down stacks, queues, trees, and graphs. Later chapters go into sorting, searching and graphing algorithms, the string-matching algorithms, and the Schonhage-Strassen integer-multiplication algorithm. Provides numerous graded exercises at the end of each chapter.


0201000296B04062001

The Design and Analysis of Computer Algorithms

Multidimensional scaling is the problem of representingn objects geometrically byn points, so that the interpoint distances correspond in some sense to experimental dissimilarities between objects. In just what sense distances and dissimilarities should correspond has been left rather vague in most approaches, thus leaving these approaches logically incomplete. Our fundamental hypothesis is that dissimilarities and distances are monotonically related. We define a quantitative, intuitively satisfying measure of goodness of fit to this hypothesis. Our technique of multidimensional scaling is to compute that configuration of points which optimizes the goodness of fit. A practical computer program for doing the calculations is described in a companion paper.

Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis

7 A Kurosh, Ringtheoretische Probleme die mit dem Burnsideschen Problem uber periodische Gruppen in Zussammenhang stehen, Bull Acad Sei URSS, Ser Math vol 5 (1941) pp 233-240 8 J Levitzki, On the radical of a general ring, Bull Amer Math Soc vol 49 (1943) pp 462^66 9 -, On three problems concerning nil rings, Bull Amer Math Soc vol 49 (1943) pp 913-919 10 -, On the structure of algebraic algebras and related rings, Trans Amer Math Soc vol 74 (1953) pp 384-409

/pdf/on-the-shortest-spanning-subtree-of-a-graph-and-the-51cl6g166z.pdf

On the shortest spanning subtree of a graph and the traveling salesman problem

We describe the numerical methods required in our approach to multi-dimensional scaling. The rationale of this approach has appeared previously.

Nonmetric multidimensional scaling: A numerical method

Three-way arrays: rank and uniqueness of trilinear decompositions, with application to arithmetic complexity and statistics

/pdf/well-quasi-ordering-the-tree-theorem-and-vazsonyi-s-23a220h9cz.pdf

Joseph B. Kruskal

Papers

Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis

On the shortest spanning subtree of a graph and the traveling salesman problem

Nonmetric multidimensional scaling: A numerical method

Three-way arrays: rank and uniqueness of trilinear decompositions, with application to arithmetic complexity and statistics

Well-quasi-ordering, the Tree Theorem, and Vazsonyi’s conjecture