With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.

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MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment

https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf

An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest.

The primary goal of pattern recognition is supervised or unsupervised classification. Among the various frameworks in which pattern recognition has been traditionally formulated, the statistical approach has been most intensively studied and used in practice. More recently, neural network techniques and methods imported from statistical learning theory have been receiving increasing attention. The design of a recognition system requires careful attention to the following issues: definition of pattern classes, sensing environment, pattern representation, feature extraction and selection, cluster analysis, classifier design and learning, selection of training and test samples, and performance evaluation. In spite of almost 50 years of research and development in this field, the general problem of recognizing complex patterns with arbitrary orientation, location, and scale remains unsolved. New and emerging applications, such as data mining, web searching, retrieval of multimedia data, face recognition, and cursive handwriting recognition, require robust and efficient pattern recognition techniques. The objective of this review paper is to summarize and compare some of the well-known methods used in various stages of a pattern recognition system and identify research topics and applications which are at the forefront of this exciting and challenging field.

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Statistical pattern recognition: a review

Principal component analysis PCA is a multivariate technique that analyzes a data table in which observations are described by several inter-correlated quantitative dependent variables. Its goal is to extract the important information from the table, to represent it as a set of new orthogonal variables called principal components, and to display the pattern of similarity of the observations and of the variables as points in maps. The quality of the PCA model can be evaluated using cross-validation techniques such as the bootstrap and the jackknife. PCA can be generalized as correspondence analysis CA in order to handle qualitative variables and as multiple factor analysis MFA in order to handle heterogeneous sets of variables. Mathematically, PCA depends upon the eigen-decomposition of positive semi-definite matrices and upon the singular value decomposition SVD of rectangular matrices. Copyright © 2010 John Wiley & Sons, Inc.

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Principal component analysis

Current efforts to reconstruct the tree of life and histories of multigene families demand the inference of phylogenies consisting of thousands of gene sequences. However, for such large data sets even a moderate exploration of the tree space needed to identify the optimal tree is virtually impossible. For these cases the neighbor-joining (NJ) method is frequently used because of its demonstrated accuracy for smaller data sets and its computational speed. As data sets grow, however, the fraction of the tree space examined by the NJ algorithm becomes minuscule. Here, we report the results of our computer simulation for examining the accuracy of NJ trees for inferring very large phylogenies. First we present a likelihood method for the simultaneous estimation of all pairwise distances by using biologically realistic models of nucleotide substitution. Use of this method corrects up to 60% of NJ tree errors. Our simulation results show that the accuracy of NJ trees decline only by ≈5% when the number of sequences used increases from 32 to 4,096 (128 times) even in the presence of extensive variation in the evolutionary rate among lineages or significant biases in the nucleotide composition and transition/transversion ratio. Our results encourage the use of complex models of nucleotide substitution for estimating evolutionary distances and hint at bright prospects for the application of the NJ and related methods in inferring large phylogenies.

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Prospects for inferring very large phylogenies by using the neighbor-joining method

The Jackknife: The Bootstrap and Other Resampling Plans.

Estimation of variance components when the design is a balanced incomplete block, the model is additive, and error, block and treatment components are normal, independent, with zero expectations, is considered using variance as a criterion. The sections are arranged in the following manner: 1—The results are summarized. 2—The notation, model, statistics and analysis of variance tables are introduced. 3—A 1–1 (linear) transformation of the sufficient statistics is performed, and a number of ‘reasonable’ estimators are constructed. 4—The model and notation are redefined in terms of matrices; and variances and covariances of the sufficient statistics are obtained. 5—A method for obtaining variances and covariances of estimators is given. 6—Variances of some of the estimators are compared, and some are seen to be inadmissible. 7—Variances of the usual variance component estimators are obtained. 8—The variances of two well-known unbiased estimators of σ2 are compared, but neither is uniformly better t...

Leone Y. Low

Papers

The Jackknife: The Bootstrap and Other Resampling Plans.

Estimators of Variance Components in the Balanced Incomplete Block Design