Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called the "discrete gamma model," uses several categories of rates to approximate the gamma distribution, with equal probability for each category. The mean of each category is used to represent all the rates falling in the category. The performance of this method is found to be quite good, and four such categories appear to be sufficient to produce both an optimum, or near-optimum fit by the model to the data, and also an acceptable approximation to the continuous distribution. The second method, called "fixed-rates model", classifies sites into several classes according to their rates predicted assuming the star tree. Sites in different classes are then assumed to be evolving at these fixed rates when other tree topologies are evaluated. Analyses of the data sets suggest that this method can produce reasonable results, but it seems to share some properties of a least-squares pairwise comparison; for example, interior branch lengths in nonbest trees are often found to be zero. The computational requirements of the two methods are comparable to that of Felsenstein's (1981, J Mol Evol 17:368-376) model, which assumes a single rate for all the sites.

/pdf/maximum-likelihood-phylogenetic-estimation-from-dna-368ndqbgd9.pdf

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

1. Introduction to wavelets 2. Review of Fourier theory and filters 3. Orthonormal transforms of time series 4. The discrete wavelet transform 5. The maximal overlap discrete wavelet transform 6. The discrete wavelet packet transform 7. Random variables and stochastic processes 8. The wavelet variance 9. Analysis and synthesis of long memory processes 10. Wavelet-based signal estimation 11. Wavelet analysis of finite energy signals Appendix. Answers to embedded exercises References Author index Subject index.

/pdf/wavelet-methods-for-time-series-analysis-1m2hg2nm53.pdf

Wavelet Methods for Time Series Analysis

Four pairwise multiple comparison procedures for the case in which the variances in the groups are unequal were compared by computer simulation: the GH procedure based on the Studentized range and the Welch formula for approximate degrees of freedom (df), the C procedure based on a weighted average of two Studentized range points, the T2 procedure based on Student's t, and the T3 procedure based on the Studentized maximum modulus. The results indicate that C, T2, and T3 have the desirable property of being conservative, whereas GH sometimes is not. Of the three conservative procedures, T3 always has shorter confidence interval length than T2, whereas C has shorter length than T3 for large df, but longer length for small df.

Pairwise Multiple Comparisons in the Unequal Variance Case

Decreased hepatotoxic bile acid composition and altered synthesis in progressive human nonalcoholic fatty liver disease

The K distribution has proven to be a promising and useful model for backscattering statistics in synthetic aperture radar (SAR) imagery. However, most studies to date have relied on a method of moments technique involving second and fourth moments to estimate the parameters of the K distribution. The variance of these parameter estimates is large in cases where the sample size is small and/or the true distribution of backscattered amplitude is highly non-Rayleigh. The present authors apply a maximum likelihood estimation method directly to the K distribution. They consider the situation for single-look SAR data as well as a simplified model for multilook data. They investigate the accuracy and uncertainties in maximum likelihood parameter estimates as functions of sample size and the parameters themselves. They also compare their results with those from a new method given by Raghavan (1991) and from a nonstandard method of moments technique; maximum likelihood parameter estimates prove to be at least as accurate as those from the other estimators in all cases tested, and are more accurate in most cases. Finally, they compare the simplified multilook model with nominally four-look SAR data acquired by the Jet Propulsion Laboratory AIRSAR over sea ice in the Beaufort Sea during March 1988. They find that the model fits data from both first-year and multiyear ice well and that backscattering statistics from each ice type are moderately non-Rayleigh. They note that the distributions for the data set differ too little between ice types to allow discrimination based on differing distribution parameters. >

Maximum likelihood estimation of K distribution parameters for SAR data

Algorithm AS 91: The Percentage Points of the χ 2 Distribution

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Algorithm AS 91: The Percentage Points of the χ 2 Distribution