Oxford Index Search Results

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Overview page. Subjects: Architecture.

[Ge]

Structural division in the length of a building or roof. The unit within a building between a pair of piers or buttresses; the division of a roof marked by its main trusses.

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Topology-Bayes versus Clade-Bayes in Phylogenetic Analysis

Ward C. Wheeler and Kurt M. Pickett.

in Molecular Biology and Evolution

February 2008; p ublished online December 2007 .

Journal Article. Subjects: Evolutionary Biology; Molecular and Cell Biology. 3422 words.

Several features of currently used Bayesian methods in phylogenetic analysis are discussed. The distinction between Clade-Bayes and Topology-Bayes is presented and illustrated with an...

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Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection

Ziheng Yang, Wendy S.W. Wong and Rasmus Nielsen.

in Molecular Biology and Evolution

April 2005; p ublished online February 2005 .

Journal Article. Subjects: Evolutionary Biology; Molecular and Cell Biology. 10544 words.

Codon-based substitution models have been widely used to identify amino acid sites under positive selection in comparative analysis of protein-coding DNA sequences. The...

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P3: Phylogenetic Posterior Prediction in RevBayes

Sebastian Höhna, Lyndon M Coghill, Genevieve G Mount, Robert C Thomson and Jeremy M Brown.

in Molecular Biology and Evolution

April 2018; p ublished online November 2017 .

Journal Article. Subjects: Evolutionary Biology; Molecular and Cell Biology. 3622 words.

Abstract

Tests of absolute model fit are crucial in model-based inference because poorly structured models can lead to biased parameter estimates. In Bayesian...

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Efficient Implementation of MrBayes on Multi-GPU

Jie Bao, Hongju Xia, Jianfu Zhou, Xiaoguang Liu and Gang Wang.

in Molecular Biology and Evolution

June 2013; p ublished online March 2013 .

Journal Article. Subjects: Evolutionary Biology; Molecular and Cell Biology. 5965 words.

MrBayes, using Metropolis-coupled Markov chain Monte Carlo (MCMCMC or (MC)3), is a popular program for Bayesian inference. As a leading method of using DNA data to infer phylogeny, the (MC)3null...

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GPU MrBayes V3.1: MrBayes on Graphics Processing Units for Protein Sequence Data

Shuai Pang, Rebecca J. Stones, Ming-Ming Ren, Xiao-Guang Liu, Gang Wang, Hong-ju Xia, Hao-Yang Wu, Yang Liu and Qiang Xie.

in Molecular Biology and Evolution

September 2015; p ublished online May 2015 .

Journal Article. Subjects: Evolutionary Biology; Molecular and Cell Biology. 1055 words.

We present a modified GPU (graphics processing unit) version of MrBayes, called ta(MC)3 (GPU MrBayes V3.1), for Bayesian phylogenetic inference on protein data sets. Our main contributions...

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A Comparative Bayes tactic for mate assessment and choice

Barney Luttbeg.

in Behavioral Ecology

January 1996; p ublished online January 1996 .

Journal Article. Subjects: Evolutionary Biology; Ecology and Conservation; Zoology and Animal Sciences. 0 words.

Models of mate choice tactics have assumed that females randomly encounter males when collecting information and the information is perfect. Empirical observations of four bird species show...

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IMEROHERPIA LAUBIERI, A NEW SOLENOGASTER FROM THE BAY OF BISCAY

CLAUDIA H. HANDL.

in Journal of Molluscan Studies

November 2002; p ublished online November 2002 .

Journal Article. Subjects: Aquatic Biology; Evolutionary Biology; Zoology and Animal Sciences. 0 words.

A new bathyal solenogaster species of the hitherto monotypic genus and monogeneric family Imeroherpia (Pachytegmentaria: Sterrofustia: Imeroherpiidae) is described from the Bay of Biscay. null...

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Accuracy and Power of Bayes Prediction of Amino Acid Sites Under Positive Selection

Maria Anisimova, Joseph P. Bielawski and Ziheng Yang.

in Molecular Biology and Evolution

June 2002; p ublished online June 2002 .

Journal Article. Subjects: Evolutionary Biology; Molecular and Cell Biology. 5932 words.

Bayes prediction quantifies uncertainty by assigning posterior probabilities. It was used to identify amino acids in a protein under recurrent diversifying selection indicated by higher...

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Use of California bay foliage by wood rats for possible fumigation of nest-borne ectoparasites

Richard B. Hemmes, Arlene Alvarado and Benjamin L. Hart.

in Behavioral Ecology

May 2002; p ublished online May 2002 .

Journal Article. Subjects: Evolutionary Biology; Ecology and Conservation; Zoology and Animal Sciences. 4780 words.

Studies were conducted to test the hypothesis that dusky-footed wood rats (Neotoma fuscipes) place bay leaves (Umbellularia californica) on or near the sleeping nest in their...

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RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

Sebastian Höhna, Michael J. Landis, Tracy A. Heath, Bastien Boussau, Nicolas Lartillot, Brian R. Moore, John P. Huelsenbeck and Fredrik Ronquist.

in Systematic Biology

July 2016; p ublished online May 2016 .

Journal Article. Subjects: Biological Sciences; Evolutionary Biology; Genetics and Genomics. 7408 words.

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number...

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Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics

Wai Lok Sibon Li and Alexei J. Drummond.

in Molecular Biology and Evolution

February 2012; p ublished online September 2011 .

Journal Article. Subjects: Evolutionary Biology; Molecular and Cell Biology. 7329 words.

We describe a procedure for model averaging of relaxed molecular clock models in Bayesian phylogenetics. Our approach allows us to model the distribution of rates of substitution across...

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HABITAT AND DIET OF EARLY STAGES OF SEPIA OFFICINALIS L. (CEPHALOPODA) IN MORBIHAN BAY, FRANCE

A. BLANC, G. PINCZON DU SEL and J. DAGUZAN.

in Journal of Molluscan Studies

August 1998; p ublished online August 1998 .

Journal Article. Subjects: Aquatic Biology; Evolutionary Biology; Zoology and Animal Sciences. 0 words.

The nursery grounds of Sepia officinalis were identified in the Gulf of Morbihan, on the Atlantic coast of France, and their abiotic and biotic features described. From the measurement of...

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Biology of the uncommon dreissenid bivalve Mytilopsis leucophaeata (Conrad, 1831) in central Chesapeake Bay

Victor S. Kennedy.

in Journal of Molluscan Studies

May 2011; p ublished online February 2011 .

Journal Article. Subjects: Aquatic Biology; Evolutionary Biology; Zoology and Animal Sciences. 8900 words.

The dark falsemussel Mytilopsis leucophaeata (Conrad, 1831) (Dreissenidae) is an uncommon epifaunal bivalve of oligohaline–mesohaline habitats in Chesapeake Bay. It is small and weakly...

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SPATIAL AND TEMPORAL VARIABILITY OF THE OPISTHOBRANCH MOLLUSCS OF PORT LLIGAT BAY, CATALONIA, NE SPAIN

A. DOMENECH, C. AVILA and M. BALLESTEROS.

in Journal of Molluscan Studies

February 2002; p ublished online February 2002 .

Journal Article. Subjects: Aquatic Biology; Evolutionary Biology; Zoology and Animal Sciences. 0 words.

Studies on the community structure and population dynamics of opisthobranchs are very scarce. This is probably related to the fact that the number of specimens is usually low and field...

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REPRODUCTIVE CYCLE OF THE CUTTLEFISH, SEPIA OFFICINALIS (L.) IN THE NORTHERN PART OF THE BAY OF BISCAY

E. GAUVRIT, R. LE GOFF and J. DAGUZAN.

in Journal of Molluscan Studies

February 1997; p ublished online February 1997 .

Journal Article. Subjects: Aquatic Biology; Evolutionary Biology; Zoology and Animal Sciences. 0 words.

The sexual cycle of the cuttlefish, Sepia officinalis, from the northern part of the Bay of Biscay was followed over several years (1988 to 1990 and 1992 to 1993). Successive maturity...

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Wood identification of Dalbergia nigra (CITES Appendix I) using quantitative wood anatomy, principal components analysis and naïve Bayes classification

Peter Gasson, Regis Miller, Dov J. Stekel, Frances Whinder and Kasia Ziemińska.

in Annals of Botany

January 2010; p ublished online November 2009 .

Journal Article. Subjects: Ecology and Conservation; Evolutionary Biology; Plant Sciences and Forestry. 6728 words.

Background and Aims

Dalbergia nigra is one of the most valuable timber species of its genus, having been traded for over 300 years. Due to...

Light-related Loci Controlling Seed Germination in Ler × Cvi and Bay-0 × Sha Recombinant Inbred-line Populations of Arabidopsis thaliana

María Paula Laserna, Rodolfo A. Sánchez and Javier F. Botto.

in Annals of Botany

October 2008; p ublished online August 2008 .

Journal Article. Subjects: Ecology and Conservation; Evolutionary Biology; Plant Sciences and Forestry. 7956 words.

Background and Aims

Dormancy is a complex trait finely regulated by hormones and environmental factors. The phytochromes that sense red:far-red (R:FR) are...

Multilocus allozyme heterozygote deficiencies in Crepidula onyx: geographic and temporal patterns among adult snails in Mission Bay, California

Lori L. Plutchak, Rachel E. Simmons and David S. Woodruff.

in Journal of Molluscan Studies

November 2006; p ublished online June 2006 .

Journal Article. Subjects: Aquatic Biology; Evolutionary Biology; Zoology and Animal Sciences. 9944 words.

Although the phenomenon of multilocus heterozygote deficiencies in numerous taxonomically diverse molluscs has been studied for over 30 years it has resisted general explanation. Here we...

Bayes’ rule and bias roles in the evolution of decision making

Sergio Castellano.

in Behavioral Ecology

January 2015; p ublished online November 2014 .

Journal Article. Subjects: Evolutionary Biology; Ecology and Conservation; Zoology and Animal Sciences. 8232 words.

Behavior is often plastic and the study of the functional basis of behavior should provide insights into the adaptive role of the mechanisms responsible for behavioral flexibility....

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ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

Andre J. Aberer, Kassian Kobert and Alexandros Stamatakis.

in Molecular Biology and Evolution

October 2014; p ublished online August 2014 .

Journal Article. Subjects: Evolutionary Biology; Molecular and Cell Biology. 2151 words.

Modern sequencing technology now allows biologists to collect the entirety of molecular evidence for reconstructing evolutionary trees. We introduce a novel, user-friendly software package...

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